Novel genes encoding proteins having prognostic, diagnostic, preventive, therapeutic, and other uses

ABSTRACT

The invention provides isolated nucleic acids encoding a variety of proteins having diagnostic, preventive, therapeutic, and other uses. These nucleic and proteins are useful for diagnosis, prevention, and therapy of a number of human and other animal disorders. The invention also provides antisense nucleic acid molecules, expression vectors containing the nucleic acid molecules of the invention, host cells into which the expression vectors have been introduced, and non-human transgenic animals in which a nucleic acid molecule of the invention has been introduced or disrupted. The invention still further provides isolated polypeptides, fusion polypeptides, antigenic peptides and antibodies. Diagnostic, screening, and therapeutic methods using compositions of the invention are also provided. The nucleic acids and polypeptides of the present invention are useful as modulating agents in regulating a variety of cellular processes.

CROSS-REFERENCE TO RELATED APPLICATIONS

[0001] This application is a continuation-in-part of U.S. applicationSer. No. 09/479,249, filed on Jan. 7, 2000, and a continuation-in-partof U.S. application Ser. No. 09/559,497, filed on Apr. 27, 2000.

[0002] This application is also a continuation-in-part of U.S.application Ser. No. 09/578,063, filed on May 24, 2000, which is acontinuation-in-part of U.S. application Ser. No. 09/333,159, filed onJun. 14, 1999.

[0003] This application is also a continuation-in-part of U.S.application Ser. No. 09/596,194, filed on Jul. 14, 2000, which is acontinuation-in-part of U.S. application Ser. No. 09/342,364, filed onJun. 29, 1999.

[0004] This application is also a continuation-in-part of U.S.application Ser. No. 09/608,452, filed on Jun. 30, 2000, which is acontinuation-in-part of U.S. application Ser. No. 09/393,996, filed onSep. 10, 1999.

[0005] This application is also a continuation-in-part of U.S.application Ser. No. 09/602,871, filed on Jun. 23, 2000, which is acontinuation-in-part of U.S. application Ser. No. 09/420,707, filed onOct. 19, 1999.

[0006] Each of the applications cross-referenced in this section areincorporated into this disclosure by reference.

STATEMENT REGARDING FEDERAL RESEARCH SUPPORT

[0007] Not Applicable

REFERENCE TO MICROFICHE APPENDIX

[0008] Not Applicable

BACKGROUND OF THE INVENTION

[0009] The molecular bases underlying many human and animalphysiological states (e.g., diseased and homeostatic states of varioustissues) remain unknown.

[0010] Nonetheless, it is well understood that these states result frominteractions among the proteins and nucleic acids present in the cellsof the relevant tissues. In the past, the complexity of biologicalsystems overwhelmed the ability of practitioners to understand themolecular interactions giving rise to normal and abnormal physiologicalstates. More recently, though, the techniques of molecular biology,transgenic and null mutant animal production, computational biology, andpharmacogenomics have enabled practitioners to discern the role andimportance of individual genes and proteins in particular physiologicalstates.

[0011] Knowledge of the sequences and other properties of genes(particularly including the portions of genes encoding proteins) and theproteins encoded thereby enables the practitioner to design and screenagents which will affect, prospectively or retrospectively, thephysiological state of an animal tissue in a favorable way. Suchknowledge also enables the practitioner, by detecting the levels of geneexpression and protein production, to diagnose the current physiologicalstate of a tissue or animal and to predict such physiological states inthe future. This knowledge furthermore enables the practitioner toidentify and design molecules which bind with the polynucleotides andproteins, in vitro, in vivo, or both.

[0012] Cadherins are a class of cell-surface adhesion molecules thatmediate calcium-dependent cell-to-cell adhesion. Many cadherins exhibithomophilic adhesion; i.e. they bind with molecules of the same cadherinon a different cell.

[0013] However, cadherins that bind specifically with other moleculeshave also been described (e.g. Telo et al., 1998, J. Biol. Chem.273:17565-17572; Ludviksson et al., 1999 J. Immunol. 162:4975-4982). Inaddition to their binding capabilities, cadherins also exhibittransmembrane signaling and regulatable adhesion activity (e.g. Yap etal., 1997, 13:119-146; Gumbiner, 2000, J. Cell Biol. 148:399-403).Despite the fact that numerous cadherins and cadherin-like proteins havebeen described, many others have not yet been characterized. A family ofcadherin-like proteins which the inventor believes to be novel isdescribed herein.

[0014] Many secreted proteins, for example, cytokines and cytokinereceptors, play a vital role in the regulation of cell growth, celldifferentiation, and a variety of specific cellular responses. A numberof medically useful proteins, including erythropoietin,granulocyte-macrophage colony stimulating factor, human growth hormone,and various interleukins, are secreted proteins. Thus, an important goalin the design and development of new therapies is the identification andcharacterization of secreted and transmembrane proteins and the geneswhich encode them.

[0015] Many secreted proteins are receptors which bind a ligand andtransduce an intracellular signal, leading to a variety of cellularresponses. The identification and characterization of such a receptorenables one to identify both the ligands which bind to the receptor andthe intracellular molecules and signal transduction pathways associatedwith the receptor, permitting one to identify or design modulators ofreceptor activity, e.g., receptor agonists or antagonists and modulatorsof signal transduction.

SUMMARY OF THE INVENTION

[0016] The present invention is based, at least in part, on thediscovery of human cDNA molecules which encode proteins which are hereindesignated TANGO 202, TANGO 210, INTERCEPT 217, TANGO 229, TANGO 234,TANGO 265, TANGO 276, TANGO 286, INTERCEPT 289, TANGO 292, TANGO 294,INTERCEPT 296, INTERCEPT 297, INTERCEPT 309, TANGO 331, TANGO 332, TANGO366, INTERCEPT 394, INTERCEPT 400, TANGO 416, MANGO 419, INTERCEPT 429,and TANGO 457. These proteins, fragments thereof, derivatives thereof,and variants thereof are collectively referred to herein as thepolypeptides of the invention or the proteins of the invention. Nucleicacid molecules encoding polypeptides of the invention are collectivelyreferred to as nucleic acids of the invention.

[0017] The nucleic acids and polypeptides of the present invention areuseful as modulating agents for regulating a variety of cellularprocesses. Accordingly, in one aspect, the present invention providesisolated nucleic acid molecules encoding a polypeptide of the inventionor a biologically active portion thereof. The present invention alsoprovides nucleic acid molecules which are suitable as primers orhybridization probes for the detection of nucleic acids encoding apolypeptide of the invention.

[0018] The invention includes fragments of any of the nucleic acidsdescribed herein wherein the fragment retains a biological or structuralfunction by which the full-length nucleic acid is characterized (e.g.,an activity, an encoded protein, or a binding capacity). The inventionfurthermore includes fragments of any of the nucleic acids describedherein wherein the fragment has a nucleotide sequence sufficiently(e.g., 50%, 60%, 70%, 80%, 85%, 90%, 95%, 98%, or 99% or greater)identical to the nucleotide sequence of the corresponding full-lengthnucleic acid that it retains a biological or structural function bywhich the full-length nucleic acid is characterized (e.g., an activity,an encoded protein, or a binding capacity).

[0019] The invention includes fragments of any of the polypeptidesdescribed herein wherein the fragment retains a biological or structuralfunction by which the full-length polypeptide is characterized (e.g., anactivity or a binding capacity). The invention furthermore includesfragments of any of the polypeptides described herein wherein thefragment has an amino acid sequence sufficiently (e.g., 50%, 60%, 70%,80%, 85%, 90%, 95%, 98%, or 99% or greater) identical to the amino acidsequence of the corresponding full-length polypeptide that it retains abiological or structural function by which the full-length polypeptideis characterized (e.g., an activity or a binding capacity).

[0020] The invention also features nucleic acid molecules which are atleast 40% (or 50%, 60%, 70%, 80%, 90%, 95%, or 98%) identical to thenucleotide sequence of any of SEQ ID NOs: 1, 2, 31, 32, 51, 52, 71, 72,81, 82, 91, 92, 96, 97, 101, 102, 106, 107, 111, 112, 121, 122, 141,142, 151, 152, 161, 162, 171, 172, 181, 182, 191, 192, 201, 202, 215,217, 221, 222, 241, 242, 251, 252, 271, 272, 279, 280, 303, 304, 308,309, 324, 325, 329, 330, 351, 352, 362, 371, 372, 379, 380, 387, 388,403, 404, 415, 416, 423, 424, 437, and 438, the TANGO 202 nucleotidesequence of the cDNA insert of a clone deposited on Apr. 21, 1999 withthe ATCC® as accession no. 207219, the TANGO 202 nucleotide sequence ofthe cDNA insert of a clone deposited on Apr. 21, 1999 with the ATCC® asaccession no. 207221, the TANGO 210 nucleotide sequence of the cDNAinsert of a clone deposited on Jul. 29, 1999 with the ATCC® as accessionno. PTA-438, the INTERCEPT 217 nucleotide sequence of the cDNA insert ofa clone deposited on May 28, 1999 with the ATCC® as accession no.PTA-147, the TANGO 229 nucleotide sequence of the cDNA insert of a clonedeposited on Oct. 1, 1999 with the ATCC® as accession no. PTA-295, theTANGO 234 nucleotide sequence of the cDNA insert of a clone deposited onApr. 2, 1999 with the ATCC® as accession no. 207184, the TANGO 265nucleotide sequence of the cDNA insert of a clone deposited on Apr. 28,1999 with the ATCC® as accession no. 207228, the TANGO 276 nucleotidesequence of the cDNA insert of a clone deposited on May 28, 1999 withthe ATCC® as accession no. PTA-150, the TANGO 286 nucleotide sequence ofthe cDNA insert of a clone deposited on Apr. 21, 1999 with the ATCC® asaccession no. 207220, the INTERCEPT 289 nucleotide sequence of the cDNAinsert of a clone deposited on Oct. 1, 1999 with the ATCC® as accessionno. PTA-295, the TANGO 292 nucleotide sequence of the cDNA insert of aclone deposited on Apr. 28, 1999 with the ATCC® as accession no. 207230,the TANGO 294 nucleotide sequence of the cDNA insert of a clonedeposited on Apr. 21, 1999 with the ATCC® as accession no. 207220, theINTERCEPT 296 nucleotide sequence of the cDNA insert of a clonedeposited on Apr. 21, 1999 with the ATCC® as accession no. 207220, theINTERCEPT 297 nucleotide sequence of the cDNA insert of a clonedeposited on May 28, 1999 with the ATCC® as accession no. PTA-147, theINTERCEPT 309 nucleotide sequence of the cDNA insert of a clonedeposited on Jan. 6, 2000 with the ATCC® as accession no. PTA-156, theTANGO 331 nucleotide sequence of the cDNA insert of a clone deposited onMay 28, 1999 with the ATCC® as accession no. PTA-147, the TANGO 332nucleotide sequence of the cDNA insert of a clone deposited on May 28,1999 with the ATCC® as accession no. PTA-151, the TANGO 366 nucleotidesequence of the cDNA insert of a clone deposited on Jul. 23, 1999 withthe ATCC® as accession no. PTA-424, the INTERCEPT 394 nucleotidesequence of the cDNA insert of a clone deposited on Jul. 23, 1999 withthe ATCC® as accession no. PTA-424, the INTERCEPT 400 nucleotidesequence of the cDNA insert of a clone deposited on Jul. 29, 1999 withthe ATCC® as accession no. PTA-438, the TANGO 416 nucleotide sequence ofthe cDNA insert of a clone deposited on Apr. 26, 1999 with the ATCC® asaccession no. PTA-1764, the MANGO 419 nucleotide sequence of the cDNAinsert of a clone deposited on Jan. 6, 2000 with the ATCC® as accessionno. PTA-1156, the INTERCEPT 429 nucleotide sequence of the cDNA insertof a clone deposited on Aug. 5, 1999 with the ATCC® as accession no.PTA-455, the TANGO 457 nucleotide sequence of the cDNA insert of a clonedeposited on Oct. 1, 1999 with the ATCC® as accession no. PTA-817, or acomplement thereof. These deposited nucleotide sequences are hereafterindividually and collectively referred to as “the nucleotide sequence ofany of the clones deposited as ATCC® Accession numbers 207184, 207219,207220, 207221, 207228, 207230, PTA-147, PTA-150, PTA-151, PTA-295,PTA-424, PTA-438, PTA-455, PTA-817, PTA-1156, and PTA-1764.”

[0021] The invention features nucleic acid molecules which include afragment of at least 15 (25, 40, 60, 80, 100, 150, 200, 250, 300, 350,400, 450, 500, 600, 700, 800, 900, 1000, 1200, 1400, 1600, 1800, 2000,2200, 2400, 2600, 2800, 3000, 3500, 4000, 4500, 5000, or more)consecutive nucleotide residues of any of SEQ ID NOs: 1, 2, 31, 32, 51,52, 71, 72, 81, 82, 91, 92, 96, 97, 101, 102, 106, 107, 111, 112, 121,122, 141, 142, 151, 152, 161, 162, 171, 172, 181, 182, 191, 192, 201,202, 215, 217, 221, 222, 241, 242, 251, 252, 271, 272, 279, 280, 303,304, 308, 309, 324, 325, 329, 330, 351, 352, 362, 371, 372, 379, 380,387, 388, 403, 404, 415, 416, 423, 424, 437, 438, and the nucleotidesequence of any of the clones deposited as ATCC® Accession numbers207184, 207219, 207220, 207221, 207228, 207230, PTA-147, PTA-150,PTA-151, PTA-295, PTA-424, PTA-438, PTA-455, PTA-817, PTA-1156, andPTA-1764, or a complement thereof.

[0022] The invention also features nucleic acid molecules which includea nucleotide sequence encoding a protein having an amino acid sequencethat is at least 50% (or 60%, 70%, 80%, 90%, 95%, or 98%) identical tothe amino acid sequence of any of SEQ ID NOs: 3-8, 33, 35, 38, 53-60,73-78, 83-85, 93-95, 98-100, 103-105, 108-110,113-115, 123-131,143-145,153-160,163,173-175, 183-185, 193-198, 203-214, 216, 223-236,243-252, 253, 273-278, 281-302, 305-307, 310-315, 326-328, 331-333,353-358, 363-368, 373-378, 381-386, 389-394, 405-414, 417-422, 425-436,and 439, or the amino acid sequence encoded by the nucleotide sequenceof any of the clones deposited as ATCC® Accession numbers 207184,207219, 207220, 207221, 207228, 207230, PTA-147, PTA-150, PTA-151,PTA-295, PTA-424, PTA-438, PTA-455, PTA-817, PTA-1156, and PTA-1764 or acomplement thereof.

[0023] In certain embodiments, the nucleic acid molecules have thenucleotide sequence of any of SEQ ID NOs: 1, 2, 31, 32, 51, 52, 71, 72,81, 82, 91, 92, 96, 97, 101, 102, 106, 107, 111, 112, 121, 122, 141,142, 151, 152, 161, 162, 171, 172, 181, 182, 191, 192, 201, 202, 215,217, 221, 222, 241, 242, 251, 252, 271, 272, 279, 280, 303, 304, 308,309, 324, 325, 329, 330, 351, 352, 362, 371, 372, 379, 380, 387, 388,403, 404, 415, 416, 423, 424, 437, 438, and the nucleotide sequence ofany of the clones deposited as ATCC® Accession numbers 207184, 207219,207220, 207221, 207228, 207230, PTA-147, PTA-150, PTA-151, PTA-295,PTA-424, PTA-438, PTA-455, PTA-817, PTA-1156, and PTA-1764.

[0024] Also within the invention are nucleic acid molecules which encodea fragment of a polypeptide having the amino acid sequence of any of SEQID NOs: 3-8, 33, 35, 38, 53-60, 73-78, 83-85, 93-95, 98-100, 103-105,108-110, 113-115, 123-131, 143-145, 153-160, 163, 173-175, 183-185,193-198, 203-214, 216, 223-236, 243-252, 253, 273-278, 281-302, 305-307,310-315, 326-328, 331-333, 353-358, 363-368, 373-378, 381-386, 389-394,405-414, 417-422, 425-436, and 439, the fragment including at least 10(12, 15, 20, 25, 30, 40, 50, 75, 100, 125, 150, 200, 250, 300, 400, 500,750, 1000 or more) consecutive amino acid residues of any of SEQ ID NOs:3-8, 33, 35, 38, 53-60, 73-78, 83-85, 93-95, 98-100, 103-105, 108-110,113-115, 123-131, 143-145, 153-160, 163, 173-175, 183-185,193-198,203-214, 216, 223-236, 243-252, 253, 273-278, 281-302, 305-307,310-315, 326-328, 331-333, 353-358, 363-368, 373-378, 381-386, 389-394,405-414, 417-422, 425-436, and 439.

[0025] The invention includes nucleic acid molecules which encode anaturally occurring allelic variant of a polypeptide comprising theamino acid sequence of any of SEQ ID NOs: 3-8, 33, 35, 38, 53-60, 73-78,83-85, 93-95, 98-100, 103-105, 108-110, 113-115, 123-131, 143-145,153-160, 163, 173-175, 183-185, 193-198, 203-214, 216, 223-236, 243-252,253, 273-278, 281-302, 305-307, 310-315, 326-328, 331-333, 353-358,363-368, 373-378, 381-386, 389-394, 405-414, 417-422, 425-436, and 439,wherein the nucleic acid molecule hybridizes under stringent conditionsto a nucleic acid molecule having a nucleic acid sequence of any of SEQID NOs: 1, 2, 31, 32, 51, 52, 71, 72, 81, 82, 91, 92, 96, 97, 101, 102,106, 107, 111, 112, 121, 122, 141, 142, 151, 152, 161, 162, 171, 172,181, 182, 191, 192, 201, 202, 215, 217, 221, 222, 241, 242, 251, 252,271, 272, 279, 280, 303, 304, 308, 309, 324, 325, 329, 330, 351, 352,362, 371, 372, 379, 380, 387, 388, 403, 404, 415, 416, 423, 424, 437,438, and the nucleotide sequence of any of the clones deposited as ATCC®Accession numbers 207184, 207219, 207220, 207221, 207228, 207230,PTA-147, PTA-150, PTA-151, PTA-295, PTA-424, PTA-438, PTA-455, PTA-817,PTA-1156, and PTA-1764, or a complement thereof.

[0026] Also within the invention are isolated polypeptides or proteinshaving an amino acid sequence that is at least about 50%, preferably60%, 75%, 90%, 95%, or 98% identical to the amino acid sequence of anyof SEQ ID NOs: 3-8, 33, 35, 38, 53-60, 73-78, 83-85, 93-95, 98-100,103-105, 108-110, 113-115, 123-131, 143-145, 153-160, 163, 173-175,183-185, 193-198, 203-214, 216, 223-236, 243-252, 253, 273-278, 281-302,305-307, 310-315, 326-328, 331-333, 353-358, 363-368, 373-378, 381-386,389-394, 405-414, 417-422, 425-436, and 439.

[0027] Also within the invention are isolated polypeptides or proteinswhich are encoded by a nucleic acid molecule having a nucleotidesequence that is at least about 40%, preferably 50%, 60%, 75%, 85%, or95% identical the nucleic acid sequence encoding any of SEQ ID NOs: 3-8,33, 35, 38, 53-60, 73-78, 83-85, 93-95, 98-100, 103-105, 108-110,113-115, 123-131, 143-145, 153-160, 163, 173-175, 183-185, 193-198,203-214, 216, 223-236, 243-252, 253, 273-278, 281-302, 305-307, 310-315,326-328, 331-333, 353-358, 363-368, 373-378, 381-386, 389-394, 405-414,417-422, 425-436, and 439, and isolated polypeptides or proteins whichare encoded by a nucleic acid molecule consisting of the nucleotidesequence which hybridizes under stringent hybridization conditions to anucleic acid molecule having the nucleotide sequence of any of SEQ IDNOs: 1, 2, 31, 32, 51, 52, 71, 72, 81, 82, 91, 92, 96, 97, 101, 102,106, 107, 111, 112, 121, 122, 141, 142, 151, 152, 161, 162, 171, 172,181, 182, 191, 192, 201, 202, 215, 217, 221, 222, 241, 242, 251, 252,271, 272, 279, 280, 303, 304, 308, 309, 324, 325, 329, 330, 351, 352,362, 371, 372, 379, 380, 387, 388, 403, 404, 415, 416, 423, 424, 437,438, and the nucleotide sequence of any of the clones deposited as ATCC®Accession numbers 207184, 207219, 207220, 207221, 207228, 207230,PTA-147, PTA-150, PTA-151, PTA-295, PTA-424, PTA-438, PTA-455, PTA-817,PTA-1156, and PTA-1764.

[0028] Also within the invention are polypeptides which are naturallyoccurring allelic variants of a polypeptide that includes the amino acidsequence of any of SEQ ID NOs: 3-8, 33, 35, 38, 53-60, 73-78, 83-85,93-95, 98-100, 103-105, 108-110, 113-115, 123-131, 143-145, 153-160,163, 173-175, 183-185, 193-198, 203-214, 216, 223-236, 243-252, 253,273-278, 281-302, 305-307, 310-315, 326-328, 331-333, 353-358, 363-368,373-378, 381-386, 389-394, 405-414, 417-422, 425-436, and 439, whereinthe polypeptide is encoded by a nucleic acid molecule which hybridizesunder stringent conditions to a nucleic acid molecule having thenucleotide sequence of any of SEQ ID NOs: 1, 2, 31, 32, 51, 52, 71, 72,81, 82, 91, 92, 96, 97, 101, 102, 106, 107, 111, 112, 121, 122, 141,142, 151, 152, 161, 162, 171, 172, 181, 182, 191, 192, 201, 202, 215,217, 221, 222, 241, 242, 251, 252, 271, 272, 279, 280, 303, 304, 308,309, 324, 325, 329, 330, 351, 352, 362, 371, 372, 379, 380, 387, 388,403, 404, 415, 416, 423, 424, 437, 438, and the nucleotide sequence ofany of the clones deposited as ATCC® Accession numbers 207184, 207219,207220, 207221, 207228, 207230, PTA-147, PTA-150, PTA-151, PTA-295,PTA-424, PTA-438, PTA-455, PTA-817, PTA-1156, and PTA-1764, or acomplement thereof.

[0029] The invention also features nucleic acid molecules that hybridizeunder stringent conditions to a nucleic acid molecule having thenucleotide sequence of any of SEQ ID NOs: 1, 2, 31, 32, 51, 52, 71, 72,81, 82, 91, 92, 96, 97, 101, 102, 106, 107, 111, 112, 121, 122, 141,142, 151, 152, 161, 162, 17.1, 172, 181, 182, 191, 192, 201, 202, 215,217, 221, 222, 241, 242, 251, 252, 271, 272, 279, 280, 303, 304, 308,309, 324, 325, 329, 330, 351, 352, 362, 371, 372, 379, 380, 387, 388,403, 404, 415, 416, 423, 424, 437, 438, and the nucleotide sequence ofany of the clones deposited as ATCC® Accession numbers 207184, 207219,207220, 207221, 207228, 207230, PTA-147, PTA-150, PTA-151, PTA-295,PTA-424, PTA-438, PTA-455, PTA-817, PTA-1156, and PTA-1764, or acomplement thereof. In some embodiments, the isolated nucleic acidmolecules encode a cytoplasmic, transmembrane, extracellular, or otherdomain of a polypeptide of the invention. In other embodiments, theinvention provides an isolated nucleic acid molecule which is antisenseto the coding strand of a nucleic acid of the invention.

[0030] Another aspect of the invention provides vectors, e.g.,recombinant expression vectors, comprising a nucleic acid molecule ofthe invention. In another embodiment, the invention provides isolatedhost cells, e.g., mammalian or non-mammalian cells, containing such avector or a nucleic acid of the invention. The invention also providesmethods for producing a polypeptide of the invention by culturing, in asuitable medium, a host cell of the invention containing a recombinantexpression vector encoding a polypeptide of the invention such that thepolypeptide of the invention is produced.

[0031] Another aspect of this invention features isolated or recombinantproteins and polypeptides of the invention. Preferred proteins andpolypeptides possess at least one biological activity possessed by thecorresponding naturally-occurring human polypeptide. An activity, abiological activity, and a functional activity of a polypeptide of theinvention refers to an activity exerted by a protein or polypeptide ofthe invention on a responsive cell as determined in vivo, or in vitro,according to standard techniques. Such activities can be a directactivity, such as an association with or an enzymatic activity exertedon a second protein or an indirect activity, such as a cellularprocesses mediated by interaction of the protein with a second protein.

[0032] The observations that expression of TANGO 416 protein isup-regulated in porcine endothelial cells, that TANGO 416 is a member ofthe cadherin family of proteins, and that at least one cadherin(designated E-cadherin), which is expressed in endothelial cells, bindsto integrin αEβ7 indicate that TANGO 416 protein can also bind withintegrin αEβ7. Thus, TANGO 416 nucleic acids, proteins, compounds whichmodulate their activity, expression, or both, and compounds (e.g.,antibodies) which bind with TANGO 416 proteins (collectively “TANGO416-related molecules”) can modulate one or more of growth,proliferation, survival, differentiation, activity, morphology, andmovement/migration of, for example, cells (e.g. endothelial cells) whichnormally express TANGO 416 and cells (e.g. certain T cells, eosinophils,mast cells, and other lymphocytes) which normally express integrin αEβ7.

[0033] The ability of TANGO 416 to bind with integrin αEβ7 indicatesthat TANGO 416 protein and other TANGO 416-related molecules can be usedto modulate the physiological activities associated with integrin αEβ7function and to treat disorders to which such physiological activitiescontribute. TANGO 416 protein can thus be involved in disorders whichaffect epithelial and lymphocytic tissues. Such disorders include cellproliferation disorders, disorders associated with aberrant epithelialpermeability, auto-, hypo-, and hyper-immune disorders, disordersassociated with aberrant binding or adhesion of cells with other cells,and inflammatory disorders.

[0034] TANGO 416-related molecules can be used to prognosticate,prevent, diagnose, or treat one or more such disorders.

[0035] The present invention is based, at least in part, on thediscovery of cDNA molecules which encode TANGO 457 proteins, which aretransmembrane proteins with one or more immunoglobulin domains and whichare encoded by sequences expressed in at least, uterus, fetal liver,fetal spleen, and placenta tissues.

[0036] The biological activities of TANGO 457 and modulators thereofinclude, e.g., (1) the ability to form, e.g., stabilize, promote,inhibit, or disrupt, protein-protein interactions (e.g., homophilicand/or heterophilic) with proteins in the signaling pathway of thenaturally-occurring polypeptide; (2) the ability to bind a ligand of thenaturally-occurring polypeptide; and (3) the ability to interact with aTANGO 457 receptor. Other activities include the ability to modulatefunction, survival, morphology, migration, proliferation and/ordifferentiation of cells of tissues (e.g., uterus, fetal liver, fetalspleen, and placenta) in which it is expressed.

[0037] TANGO 229, compounds which modulate its activity, expression, orboth, and compounds which interact with TANGO 229 can exhibit theability to affect one or more of growth, proliferation, survival,differentiation, activity, morphology, and movement/migration of, forexample, T cells and cells of heart, liver, pancreas, placenta, brainlung, skeletal muscle, kidney, spleen, lymph node, peripheral bloodleukocyte, bone marrow, and thymus tissues. TANGO 229 protein can beinvolved in mediating cell binding and adhesion, includingbinding/adhesion of cells with other cells, with extracellular matrix,and with foreign materials. TANGO 229 protein can thus have a role indisorders associated with aberrant binding of these types. TANGO 229protein can also be involved in mediating attraction and repulsion ofcells and translocation of cells through, past, or along other cells ortissues. TANGO 229 protein can furthermore be involved in transducingsignals across the cell membrane.

[0038] INTERCEPT 289, compounds which modulate its activity, expression,or both, and compounds which interact with INTERCEPT 289 can exhibit theability to affect one or more of growth, proliferation, survival,differentiation, activity, morphology, and movement/migration of, forexample, lymphocytes such as monocytes and macrophages. INTERCEPT 289protein can be involved in activating one or more types of macrophagesand monocytes, and thus can be involved in one or more immune disordersand other types of disorders mediated by monocytes and macrophages.

[0039] INTERCEPT 309, compounds which modulate its activity, expression,or both, and compounds which interact with INTERCEPT 309 modulate one ormore of growth, proliferation, survival, differentiation, activity,morphology, and movement/migration of cells of brain, liver, colon,prostate, kidneys, thyroid, and other epithelial and endothelialtissues. INTERCEPT 309 is a claudin-like protein, and can modulatetight-junction regulated intercellular and paracellular diffusion.INTERCEPT 309 also can participate in cell-to-cell adhesive mechanismsthat do not necessarily involve tight junction formation. In addition,INTERCEPT 309 can mediate interaction of cells in which it is expressedwith Clostridium perfringens enterotoxin, and can thus be involved indisorders mediated by C. perfringens and other pathogens. Furthermore,INTERCEPT 309 is associated with normal and aberrant apoptosis, and thuswith disorders associated with aberrant apoptosis.

[0040] MANGO 419, compounds which modulate its activity, expression, orboth, and compounds which interact with MANGO 419 can modulate one ormore of growth, proliferation, survival, differentiation, activity,morphology, and movement/migration of, for example, cells of embryonicand mammary, prostate, and other epithelial and endothelial tissues.MANGO 419 protein can be involved in disorders which affect epithelialand endothelial tissues. Such disorders include cell proliferationdisorders, disorders associated with aberrant epithelial/endothelialpermeability, and disorders associated with aberrant binding or adhesionof cells with other cells, with extracellular matrix, or with foreignmaterials.

[0041] INTERCEPT 429, compounds which modulate its activity, expression,or both, and compounds which interact with INTERCEPT 429 can modulateone or more of growth, proliferation, survival, differentiation,activity, morphology, and movement/migration of, for example, cells ofcardiac muscle, small intestine, and one or more of fetal lung, testis,and B cell tissues. INTERCEPT 429 can be involved in modulating growth,proliferation, survival, differentiation, and activity of cells of thesetissues, in both normal and diseased tissues.

[0042] TANGO 210, compounds which modulate its activity, expression, orboth, and compounds which interact with TANGO 210 exhibit the ability toaffect one or more of growth, proliferation, survival, differentiation,activity, morphology, and movement/migration of, for example, humanadult kidney, fetal kidney, skin, and bone marrow cells and tissues.TANGO 210 modulates the structure of extracellular matrix within, or influid communication with, one or more of these tissues. For example,TANGO 210 exhibits proteinase activity that can enzymatically degradeone or more of the proteinaceous components of extracellular matrix.Thus, TANGO 210-related molecules can be used to prognosticate, prevent,diagnose, or treat disorders relating to aberrant formation ordegradation of extracellular matrix. In various embodiments, forexample, TANGO 210 is used to prognosticate, prevent, diagnose, or treatkidney, bone marrow, and skin disorders. TANGO 210 can also be used toprognosticate, prevent, diagnose, or treat one or more cancers,including metastatic cancers.

[0043] TANGO 366, compounds which modulate its activity, expression, orboth, and compounds which interact with TANGO 366 modulate one or moreof growth, proliferation, survival, differentiation, activity,morphology, and movement/migration of human fibroblast cells and tissuesin which fibroblasts normally or aberrantly occur. TANGO 366 is a cellsurface protein-binding protein. TANGO 366 modulates binding of a cellwhich expresses it with one or more of an extracellular fluid protein, aprotein component of the extracellular matrix, a surface protein anothercell of the same animal, and a surface protein of a bacterium, fungus,or virus. TANGO 366 is therefore involved in cell-to-cell adhesion,tissue and extracellular matrix invasivity of cells, infectivity ofcells by pathogens such as bacteria and viruses, endocrine signalingprocesses, tissue developmental and organizational processes, and thelike.

[0044] INTERCEPT 394, compounds which modulate its activity, expression,or both, and compounds which interact with INTERCEPT 394 modulate one ormore of growth, proliferation, survival, differentiation, activity,morphology, and movement/migration of, for example, human adult andfetal kidney cells and tissues. INTERCEPT 394, a transmembrane protein,is involved in modulation of intracellular processes, includingmodulation that is effected upon binding of a ligand to an extracellularportion of INTERCEPT 394. INTERCEPT 394 protein is thus capable oftransmitting signals across a membrane (e.g., from a signal sourceoutside the cell to a molecule within the cell or from a signal sourcewithin the cell to a molecule outside the cell), along a membrane (i.e.,between two or more molecules on a single side of a membrane), andcombinations thereof. INTERCEPT 394 protein is also capable ofinteracting with other membrane-associated proteins to form complexes,the activity or specificity of which can be affected by association ofINTERCEPT 394 therewith.

[0045] INTERCEPT 400, compounds which modulate its activity, expression,or both, and compounds which interact with INTERCEPT 400 modulate one ormore of growth, proliferation, survival, differentiation, activity,morphology, and movement/migration of, for example, human adult andfetal keratinocytes and brain cells and tissues. INTERCEPT 400 is atransmembrane protein that is involved in modulating interactionsbetween membrane components and cellular cytoskeletons, such asinteractions involved in activation of leukocytes, interactions involvedin affecting cellular metabolism, interactions involved in cellulargrowth, and interactions involved in cellular proliferation.

[0046] INTERCEPT 217 polypeptides, nucleic acids, and modulators thereofexhibit the ability to affect growth, proliferation, survival,differentiation, and activity of human pancreas, skeletal muscle, heart,brain, placenta, lung, liver, and kidney cells. INTERCEPT 217 modulatescellular binding to one or more mediators, modulates activity andrelease of one or more pancreatically secreted digestive enzymes, andprotects tissue from endogenous digestive enzymes. INTERCEPT 217polypeptides, nucleic acids, and modulators thereof can be used toprevent, diagnose, or treat disorders relating to aberrant endogenousdigestive enzyme activity, inappropriate interaction (ornon-interaction) of cells with mediators, inappropriate cellulardevelopment and proliferation, inappropriate inflammation, andinappropriate immune responses.

[0047] INTERCEPT 297 polypeptides, nucleic acids, and modulators thereofexhibit the ability to affect growth, proliferation, survival,differentiation, and activity of human fetal cells and spleen cells andof (e.g., bacterial or fungal) cells and viruses which infect humans.Furthermore, INTERCEPT 297 modulates organization, structure, andfunction of biological membranes. INTERCEPT 297 polypeptides, nucleicacids, and modulators thereof can be used to affect development andpersistence of atherogenesis and arteriosclerosis, for example, or tomodulate transmembrane transport processes such as ion transport acrossneuronal and muscle cell membranes.

[0048] TANGO 276 polypeptides, nucleic acids, and modulators thereofmodulate growth, proliferation, survival, differentiation, and activityof human heart, placenta, brain, lung, liver, skin, kidney, pancreas,spleen, and fetal tissues. TANGO 276 guides neuronal growth anddevelopment and modulates growth, homeostasis, and regeneration of otherepithelial tissues. TANGO 276 is a secreted protein which mediatescellular interaction with cells, molecules, and structures (e.g.,extracellular matrix) in the extracellular environment. TANGO 276 isinvolved in growth, organization, migration, and adhesion of tissues andthe cells which constitute those tissues. Furthermore, TANGO 276modulates growth, proliferation, survival, differentiation, and activityof neuronal cells and immune system cells.

[0049] TANGO 292 polypeptides, nucleic acids, and modulators thereofmodulate growth, proliferation, survival, differentiation, and activityof human keratinocytes, including embryonic keratinocytes. TANGO 292, atransmembrane protein, is also involved in binding and uptake of calciumand other metal ions, and in responses of cells which express it to thepresence and uptake of such ions. TANGO 292 polypeptides, nucleic acids,and modulators can be used to prevent, diagnose, and treat disordersinvolving one or more of bone uptake, maintenance, and deposition,formation, maintenance, and repair of cartilage and skin, formation andmaintenance of extracellular matrices, movement of cells throughextracellular matrices, coagulation and dissolution of blood components,and deposition of materials in and on arterial walls.

[0050] TANGO 331 polypeptides, nucleic acids, and modulators thereofmodulate growth, proliferation, survival, differentiation, and activityof human fetal, lung, spleen, and thymus cells and tissues. As describedherein, TANGO 331 is involved in physiological activities such asmaintenance of epithelia, carcinogenesis, modulation and storage ofprotein factors and metals, lactation, and infant nutrition. TANGO 331also modulates cellular binding and uptake of cytokines, growth factors,and metal ions.

[0051] TANGO 332 polypeptides, nucleic acids, and modulators thereofmodulate growth, proliferation, survival, differentiation, and activityof human brain and other tissues. As described herein, TANGO 332 isinvolved in modulating establishment and maintenance of neuralconnections, cell-to-cell adhesion, tissue and extracellular matrixinvasivity, and the like.

[0052] TANGO 202 exhibits the ability to affect growth, proliferation,survival, differentiation, and activity of human hematopoietic cells(e.g., bone marrow stromal cells) and fetal cells. TANGO 202 modulatescellular binding to one or more mediators, modulates proteolyticactivity in vivo, modulates developmental processes, and modulates cellgrowth, proliferation, survival, differentiation, and activity.

[0053] TANGO 234 exhibits the ability to affect growth, proliferation,survival, differentiation, and activity of human lung, hematopoietic,and fetal cells and of (e.g., bacterial or fungal) cells and viruseswhich infect humans. TANGO 234 modulates growth, proliferation,survival, differentiation, and activity of gamma delta T cells, forexample. Furthermore, TANGO 234 modulates cholesterol deposition onhuman arterial walls, and is involved in uptake and metabolism of lowdensity lipoprotein and regulation of serum cholesterol levels.

[0054] TANGO 265 modulates growth and regeneration of neuronal andepithelial tissues, and guides neuronal axon development. TANGO 265 is atransmembrane protein which mediates cellular interaction with cells,molecules and structures (e.g., extracellular matrix) in theextracellular environment. TANGO 265 is involved in growth,organization, and adhesion of tissues and the cells which constitutethose tissues. Furthermore, TANGO 265 modulates growth, proliferation,survival, differentiation, and activity of neuronal cells and immunesystem cells.

[0055] TANGO 286 protein is involved in lipid-binding physiologicalprocesses such as lipid transport, metabolism, serum lipid particleregulation, host anti-microbial defensive mechanisms, and the like.

[0056] TANGO 294 protein is involved in facilitating absorption andmetabolism of fat. Disorders which can be modulated by TANGO 294proteins, nucleic acids, and compounds that interact with them include,for example, inadequate expression of gastric/pancreatic lipase, cysticfibrosis, exocrine pancreatic insufficiency, medical treatments whichalter fat absorption, and obesity.

[0057] INTERCEPT 296 protein is involved in physiological processesrelated to disorders of the human lung and esophagus. Disorders whichcan be modulated by INTERCEPT 296 proteins, nucleic acids, and compoundsthat interact with them include, for example, various cancers,bronchitis, cystic fibrosis, respiratory infections (e.g., influenza,bronchiolitis, pneumonia, and tuberculosis), asthma, emphysema, chronicbronchitis, bronchiectasis, pulmonary edema, pleural effusion, pulmonaryembolus, adult and infant respiratory distress syndromes, heartburn, andgastric esophageal reflux disease.

[0058] In one embodiment, a polypeptide of the invention has an aminoacid sequence sufficiently identical to a polypeptide of the inventionor to an identified domain thereof. As used herein, the term“sufficiently identical” refers to a first amino acid or nucleotidesequence which contains a sufficient or minimum number of identical orequivalent (e.g., with a similar side chain) amino acid residues ornucleotides to a second amino acid or nucleotide sequence such that thefirst and second amino acid or nucleotide sequences have a common domainand/or common functional activity. For example, amino acid or nucleotidesequences which contain a common domain having about 65% identity,preferably 75% identity, more preferably 85%, 95%, or 98% identity aredefined herein as sufficiently identical.

[0059] In one embodiment, the isolated polypeptide of the inventionlacks both a transmembrane and a cytoplasmic domain. In anotherembodiment, the polypeptide lacks both a transmembrane domain and acytoplasmic domain and is soluble under physiological conditions.

[0060] The polypeptides of the present invention, or biologically activeportions thereof, can be operably linked with a heterologous amino acidsequence to form fusion proteins. The invention further featuresantibody substances that specifically bind a polypeptide of theinvention, such as monoclonal or polyclonal antibodies, antibodyfragments, and single-chain antibodies. In addition, the polypeptides ofthe invention or biologically active portions thereof can beincorporated into pharmaceutical compositions, which optionally includepharmaceutically acceptable carriers. These antibody substances can bemade, for example, by providing the polypeptide of the invention to animmunocompetent vertebrate and thereafter harvesting blood or serum fromthe vertebrate.

[0061] In another aspect, the present invention provides methods fordetecting the presence of the activity or expression of a polypeptide ofthe invention in a biological sample by contacting the biological samplewith an agent capable of detecting an indicator of activity such thatthe presence of activity is detected in the biological sample.

[0062] In another aspect, the invention provides methods for modulatingactivity of a polypeptide of the invention comprising contacting a cellwith an agent that modulates (inhibits or enhances) the activity orexpression of a polypeptide of the invention such that activity orexpression in the cell is modulated. In one embodiment, the agent is anantibody that specifically binds with a polypeptide of the invention.

[0063] In another embodiment, the agent modulates expression of apolypeptide of the invention by modulating transcription, splicing, ortranslation of an mRNA encoding a polypeptide of the invention. In yetanother embodiment, the agent is a nucleic acid molecule having anucleotide sequence that is antisense with respect to the coding strandof an mRNA encoding a polypeptide of the invention.

[0064] The present invention also provides methods of treating a subjecthaving a disorder characterized by aberrant activity of a polypeptide ofthe invention or aberrant expression of a nucleic acid of the inventionby administering an agent which is a modulator of the activity of apolypeptide of the invention or a modulator of the expression of anucleic acid of the invention to the subject. In one embodiment, themodulator is a protein of the invention. In another embodiment, themodulator is a nucleic acid of the invention. In other embodiments, themodulator is a peptide, peptidomimetic, or other small molecule. In yetanother embodiment, the modulator is an antibody.

[0065] The present invention also provides diagnostic assays foridentifying the presence or absence of a genetic lesion or mutationcharacterized by at least one of: (i) aberrant modification or mutationof a gene encoding a polypeptide of the invention, (ii) mis-regulationof a gene encoding a polypeptide of the invention, and (iii) aberrantpost-translational modification of a polypeptide of the inventionwherein a wild-type form of the gene encodes a polypeptide having theactivity of the polypeptide of the invention.

[0066] In another aspect, the invention provides a method foridentifying a compound that binds with or modulates the activity of apolypeptide of the invention. In general, such methods entail measuringa biological activity of the polypeptide in the presence and absence ofa test compound and identifying those compounds which bind with or alterthe activity of the polypeptide.

[0067] The invention also features methods for identifying a compoundwhich modulates the expression of a polypeptide or nucleic acid of theinvention by measuring the expression of the polypeptide or nucleic acidin the presence and absence of the compound.

[0068] Other features and advantages of the invention will be apparentfrom the following detailed description and claims.

BRIEF DESCRIPTION OF THE DRAWINGS

[0069]FIG. 1 comprises FIGS. 1A through 1I. The nucleotide sequence (SEQID NO: 1) of a cDNA encoding the human TANGO 416 protein describedherein is listed in FIGS. 1A through 1I. The open reading frame (ORF;residues 376 to 3780; SEQ ID NO: 2) of the cDNA is indicated bynucleotide triplets, above which the amino acid sequence (SEQ ID NO: 3)of human TANGO 416 is listed.

[0070]FIG. 2 comprises FIGS. 2A through 2I. The nucleotide sequence (SEQID NO: 31) of a cDNA encoding the human TANGO 416 protein describedherein is listed in FIGS. 2A through 2I. The open reading frame (ORF;residues 376 to 3777; SEQ ID NO: 32) of the cDNA is indicated bynucleotide triplets, above which the amino acid sequence (SEQ ID NO: 33)of human TANGO 416 is listed.

[0071]FIG. 3 is a hydrophobicity plot of the embodiment of human TANGO416 protein listed in FIG. 1. In the hydrophobicity plots disclosedherein, the locations of cysteine residues (“Cys”) and potentialN-glycosylation sites (“Ngly”) are indicated by vertical bars and thepredicted extracellular (“out”), intracellular (“ins”), or transmembrane(“TM”) portions of the protein backbone are indicated by a horizontalbar. Relatively hydrophobic regions of the protein are above the dashedhorizontal line, and relatively hydrophilic regions of the protein arebelow the dashed horizontal line.

[0072]FIG. 4 is an alignment of a portion of the TANGO 416 cDNA sequence(“T416”; residues 1651-4000 of SEQ ID NO: 1) with a human testis cDNAclone having GenBank accession number AL137471 (“AL137471”; SEQ ID NO:40). This alignment indicates that the two nucleotide sequences areabout 98.6% identical over the overlapping region. The alignment wasmade using the ALIGN software (BLOSUM62 scoring matrix, gap openingpenalty 12, gap extension penalty 4, frameshift gap penalty 5). In thealignments in this disclosure, similar residues are indicated by “.”,and identical residues are indicated by “:” or “i”.

[0073]FIG. 5 is an alignment of a portion of the TANGO 416 ORFnucleotide sequence (“T416”; residues 1-3405 of SEQ ID NO: 2) with theORF nucleotide sequence (“m-PC”; SEQ ID NO: 41) of murine protocadherin(sometimes designated vascular endothelial cadherin-2 or mVE-cad-2).This alignment indicates that the two nucleotide sequences are about55.4% identical over the overlapping region. The alignment was madeusing the ALIGN-software (BLOSUM62 scoring matrix, gap opening penalty12, gap extension penalty 4, frameshift gap penalty 5).

[0074]FIG. 6 is an alignment of a portion of the TANGO 416 protein aminoacid sequence (“T416”; residues 1-1135 of SEQ ID NO: 3) with the aminoacid sequence (“m-PC”; SEQ ID NO: 42) of murine protocadherin. Thisalignment indicates that the two amino acid sequences are about 32.8%identical over the overlapping region. The alignment was made using theALIGN software (BLOSUM62 scoring matrix, gap opening penalty 12, gapextension penalty 4).

[0075]FIGS. 7A through 7D depict a cDNA sequence of human TANGO 457 (SEQID NO: 51) and the predicted human TANGO 457 amino acid sequence encodedby the sequence (SEQ ID NO: 53). The open reading frame of TANGO 457,comprises nucleotide 149 to nucleotide 1243 of SEQ ID NO: 51 (SEQ ID NO:52).

[0076]FIG. 8 depicts a hydrophobicity plot of human TANGO 457.

[0077]FIGS. 9A through 9D depict a local alignment of the nucleic acidof human TANGO 457 shown in SEQ ID NO: 51 and a portion of thenucleotide sequence of human chromosome 11p4.3 PAC clone pDJ239b22, fromnucleic acids 121077 to 122478 (SEQ ID NO: 61; accession numberAC003969). In the alignment, the TANGO 457 sequence is the top strand,and the 11p14.3 PAC clone pDJ239b22 sequences is on the bottom. Thealignment shows that there is 100% nucleotide sequence identity betweenthe TANGO 457 sequence of SEQ ID NO: 51 and human chromosome 11p14.3 PACclone pDJ239b22, from nucleotides 908 to 2305 of TANGO 457. Thisalignment was performed using the ALIGN alignment program with a PAM120scoring matrix, a gap length penalty of 12, and a gap penalty of 4.

[0078]FIG. 10 comprises FIGS. 10A through 10G. The nucleotide sequence(SEQ ID NO: 71) of a cDNA encoding the human TANGO 229 protein describedherein is listed in FIGS. 10A through 10F. The open reading frame (ORF;residues 72 to 2216; SEQ ID NO: 72) of the cDNA is indicated bynucleotide triplets, above which the amino acid sequence (SEQ ID NO: 73)of human TANGO 229 is listed.

[0079]FIG. 10G is a hydrophobicity plot of one embodiment of human TANGO229 protein.

[0080]FIG. 11 comprises FIGS. 11A through 11Z-6.

[0081] The nucleotide sequence (SEQ ID NO: 81) of a cDNA encoding form1a of the human INTERCEPT 289 protein described herein is listed inFIGS. 11A through 11C. The ORF (residues 179 to 742; SEQ ID NO: 82) ofthe cDNA is indicated by nucleotide triplets, above which the amino acidsequence (SEQ ID NO: 83) of form 1a of human INTERCEPT 289 is listed.

[0082] The nucleotide sequence (SEQ ID NO: 91) of a cDNA encoding form1b of human INTERCEPT 289 protein described herein is listed in FIGS.11D through 11G. The ORF (residues 179 to 712; SEQ ID NO: 92) of thecDNA is indicated by nucleotide triplets, above which the amino acidsequence (SEQ ID NO: 93) of form 1 b of human INTERCEPT 289 is listed.

[0083] The nucleotide sequence (SEQ ID NO: 96) of a cDNA encoding form2a of human INTERCEPT 289 protein described herein is listed in FIGS.11H through 11K. The ORF (residues 162 to 656; SEQ ID NO: 97) of thecDNA is indicated by nucleotide triplets, above which the amino acidsequence (SEQ ID NO: 98) of form 2a of human INTERCEPT 289 is listed.

[0084] The nucleotide sequence (SEQ ID NO: 101) of a cDNA encoding form2b of human INTERCEPT 289 protein described herein is listed in FIGS.11L through 11O. The ORF (residues 162 to 626; SEQ ID NO: 102) of thecDNA is indicated by nucleotide triplets, above which the amino acidsequence (SEQ ID NO: 103) of form 2 b of human INTERCEPT 289 is listed.

[0085] The nucleotide sequence (SEQ ID NO: 106) of a cDNA encoding form3a of human INTERCEPT 289 protein described herein is listed in FIGS.11P through 11S. The ORF (residues 162 to 596; SEQ ID NO: 107) of thecDNA is indicated by nucleotide triplets, above which the amino acidsequence (SEQ ID NO: 108) of form 3a of human INTERCEPT 289 is listed.

[0086] The nucleotide sequence (SEQ ID NO: 111) of a cDNA encoding form3b of human INTERCEPT 289 protein described herein is listed in FIGS.11T through 11V. The ORF (residues 162 to 566; SEQ ID NO: 112) of thecDNA is indicated by nucleotide triplets, above which the amino acidsequence (SEQ ID NO: 113) of form 3b of human INTERCEPT 289 is listed.

[0087]FIG. 11W is an alignment, made using the Wisconsin™ BestFitsoftware (Smith and Waterman, (1981) Adv. Appl. Math. 2:482-489;BLOSUM62 scoring matrix, gap opening penalty 10/gap extension penalty10) of the amino acid sequences of murine myeloid DNAX accessory proteinassociated lectin-1 (“M”; MDL-1; SEQ ID NO: 88), murine INTERCEPT 289(“R”; SEQ ID NO: 163), human MDL-1 (“H”; SEQ ID NO: 86), form 1a ofINTERCEPT 289 (“A”; SEQ ID NO: 83), form 1b of INTERCEPT 289 (“B”; SEQID NO: 93), form 2a of INTERCEPT 289 (“C”; SEQ ID NO: 98), form 2b ofINTERCEPT 289 (“D”; SEQ ID NO: 103), form 3a of INTERCEPT 289 (“E”; SEQID NO: 108), and form 3b of INTERCEPT 289 (“F”; SEQ ID NO: 113).

[0088] FIGS. 11X-6 through 11X-14 is an alignment (made using theWisconsin™ BestFit software; Smith and Waterman, (1981) Adv. Appl. Math.2:482-489; gap opening penalty 10/gap extension penalty 10), of thenucleotide sequences of cDNA molecules encoding form 1a of INTERCEPT 289(“A”; SEQ ID NO: 81), form 1b of INTERCEPT 289 (“B”; SEQ ID NO: 91),form 2a of INTERCEPT 289 (“C”; SEQ ID NO: 96), form 2b of INTERCEPT 289(“D”; SEQ ID NO: 101), form 3a of INTERCEPT 289 (“E”; SEQ ID NO: 106),and form 3b of INTERCEPT 289 (“F”; SEQ ID NO: 111).

[0089] FIGS. 11Y-1 through 11Y-6 is a series of hydrophobicity plots forindividual forms of human INTERCEPT 289 protein. The plot correspondingto form 1a is shown in FIG. 11Y-1. The plot corresponding to form 1b isshown in FIG. 1Y-2. The plot corresponding to form 2a is shown in FIG.1Y-3. The plot corresponding to form 2b is shown in FIG. 11Y-4. The plotcorresponding to form 3a is shown in FIG. 11Y-5. The plot correspondingto form 3b is shown in FIG. 1Y-6.

[0090] The nucleotide sequence (SEQ ID NO: 161) of a cDNA encodingmurine INTERCEPT 289 protein described herein is listed in FIGS. 1Z-1through 11Z-3.

[0091] The ORF (residues 198 to 767; SEQ ID NO: 162) of the cDNA isindicated by nucleotide triplets, beneath which the amino acid sequence(SEQ ID NO: 163) of murine INTERCEPT 289 is listed. FIGS. 11Z-4 and11Z-5 are a manual alignment of the nucleotide sequences of murineINTERCEPT 289 ORF (“M1289”; SEQ ID NO: 162) and the ORF of form 1a ofhuman INTERCEPT 289 (“HI289”; SEQ ID NO: 82). FIG. 11Z-6 is ahydrophobicity plot for murine INTERCEPT 289 protein.

[0092]FIG. 12 comprises FIGS. 12A through 12T. The nucleotide sequence(SEQ ID NO: 121) of a cDNA encoding the human INTERCEPT 309 proteindescribed herein is listed in FIGS. 12A through 12C. The ORF (residues 2to 646; SEQ ID NO: 122) of the cDNA is indicated by nucleotide triplets,above which the amino acid sequence (SEQ ID NO: 123) of human INTERCEPT309 is listed. FIG. 12D is a hydrophobicity plot of human INTERCEPT 309protein. An alignment (made using the ALIGN software; pam120.mat scoringmatrix, gap opening penalty=12, gap extension penalty=4) of thenucleotide sequences of a cDNA clone (“DKFZ”; SEQ ID NO: 134; GenBankaccession no. AL049977) obtained from human fetal brain tissue andINTERCEPT 309 cDNA (“1309”; SEQ ID NO: 121) is shown in FIGS. 12Ethrough 12K. An alignment (made using the ALIGN software; pam120.matscoring matrix, gap opening penalty=12, gap extension penalty=4) of thenucleotide sequences of the cDNA encoding human INTERCEPT 309 (“1309”;SEQ ID NO: 121) and a portion of a cDNA encoding murine claudin-8protein (“CLAUD8”; SEQ ID NO: 132) is shown in FIGS. 12L through 12R. Analignment (made using the ALIGN software; pam120.mat scoring matrix, gapopening penalty=12, gap extension penalty=4) of the amino acid sequencesof human INTERCEPT 309 protein (“1309”; SEQ ID NO: 123) and murineclaudin-8 protein (“CLAUD8”; SEQ ID NO: 133) is shown in FIG. 12S. Amanual alignment of individual alignments (made using the Wisconsin™BestFit software; Smith and Waterman (1981) Adv. Appl. Math. 2:482-489;blosum62 scoring matrix, gap opening penalty 10/gap extension penalty10) of the amino acid sequences of human INTERCEPT 309 protein (“1309”;SEQ ID NO: 123) with each of human Clostridium perfringens enterotoxinreceptor (“hCPE”; SEQ ID NO: 135), murine C. perfringens enterotoxinreceptor (“mCPE”; SEQ ID NO: 136), and a protein encoded by a cDNArecovered from regressing rat ventral prostate tissue (“rRPV”; SEQ IDNO: 137) is shown in FIG. 12T.

[0093]FIG. 13 comprises FIGS. 13A and 13B. The nucleotide sequence (SEQID NO: 141) of a cDNA encoding the human MANGO 419 protein describedherein is listed in FIG. 13A. The ORF (residues 84 to 323; SEQ ID NO:142) of the cDNA is indicated by nucleotide triplets, above which theamino acid sequence (SEQ ID NO: 143) of human MANGO 419 is listed. FIG.13B is a hydrophobicity plot of human MANGO 419 protein.

[0094]FIG. 14 comprises FIGS. 14A and 14B. The nucleotide sequence (SEQID NO: 151) of a cDNA encoding the human INTERCEPT 429 protein describedherein is listed in FIG. 14A. The ORF (residues 95 to 439; SEQ ID NO:152) of the cDNA is indicated by nucleotide triplets, above which theamino acid sequence (SEQ ID NO: 153) of human INTERCEPT 429 is listed.FIG. 14B is a hydrophobicity plot of human INTERCEPT 429 protein.

[0095]FIG. 15 comprises FIGS. 15A through 15Y. The nucleotide sequence(SEQ ID NO: 171) of a cDNA encoding the human TANGO 210 proteindescribed herein is listed in FIGS. 15A, 15B, 15C, and 15D. The openreading frame (ORF; residues 45 to 1583; SEQ ID NO: 172) of the cDNA isindicated by nucleotide triplets, above which the amino acid sequence(SEQ ID NO: 173) of human TANGO 210 is listed. FIG. 15E is ahydrophobicity plot of human TANGO 210 protein (the conformation of thealternative form of TANGO 210 protein, wherein the carboxyl terminalportion comprises a transmembrane domain, is shown here). The nucleotidesequence (SEQ ID NO: 181) of a cDNA encoding the murine TANGO 210protein described herein is listed in FIGS. 15F, 15G, 15H, and 151. TheORF (residues 22 to 927 and 1280 to 1906; collectively, SEQ ID NO: 182)of the cDNA is indicated by nucleotide triplets, above which the aminoacid sequence (SEQ ID NO: 183) of murine TANGO 210 is listed. FIG. 15Jis a hydrophobicity plot of murine TANGO 210 protein. An alignment ofthe amino acid sequences of human TANGO 210 protein (SEQ ID NO: 173) andmurine TANGO 210 protein (SEQ ID NO: 183) amino acid sequences is shownin FIGS. 15K and 15L, wherein identical amino acid residues areindicated by “:” and similar amino acid residues are indicated by “.”.An alignment of the nucleotide sequences of the human (SEQ ID NO: 171)and murine (SEQ ID NO: 181) cDNAs encoding TANGO 210 protein is shown inFIGS. 15M through 15U. FIGS. 15V and 15W are an alignment of the aminoacid sequences of human TANGO 210 protein (“210”; SEQ ID NO: 173) andhuman matrix metalloproteinase-8 (MMP-8; “MMP-8”; SEQ ID NO: 176). Analignment of the nucleotide sequences of the open reading frame (ORF)encoding human TANGO 210 (“210”; SEQ ID NO: 172) and the ORF encodinghuman MMP-8 (SEQ ID NO: 177) is shown in FIGS. 15X-1 through 15X-6. FIG.15Y is a graph which depicts expression of TANGO 210 mRNA in selectedhuman tissue and cell types, relative to TANGO 210 expression in thehuman fetal heart tissue.

[0096]FIG. 16 comprises FIGS. 16A through 16E. The nucleotide sequence(SEQ ID NO: 191) of a cDNA encoding the human TANGO 366 proteindescribed herein is listed in FIGS. 16A through 16D. The ORF (residues86 to 1144; SEQ ID NO: 192) of the cDNA is indicated by nucleotidetriplets, above which the amino acid sequence (SEQ ID NO: 193) of humanTANGO 366 is listed. FIG. 16E is a hydrophobicity plot of human TANGO366 protein.

[0097]FIG. 17 comprises FIGS. 17A through 17M. The nucleotide sequence(SEQ ID NO: 201) of a cDNA encoding the human INTERCEPT 394 proteindescribed herein is listed in FIGS. 17A through 17F. The ORF (residues320 to 2653; SEQ ID NO: 202) of the cDNA is indicated by nucleotidetriplets, above which the amino acid sequence (SEQ ID NO: 203) of humanINTERCEPT 394 is listed. FIG. 17G is a hydrophobicity plot of humanINTERCEPT 394 protein. The nucleotide sequence (SEQ ID NO: 201) of acDNA encoding the human INTERCEPT 394 protein described herein is listedin FIGS. 17H through 17M. The alternative ORF (residues 120 to 2567; SEQID NO: 215) of the cDNA is indicated by nucleotide triplets, above whichthe amino acid sequence (SEQ ID NO: 216) of this alternative form ofhuman INTERCEPT 394 protein is listed.

[0098]FIG. 18 comprises FIGS. 18A through 18R. The nucleotide sequence(SEQ ID NO: 221) of a cDNA encoding the human INTERCEPT 400 proteindescribed herein is listed in FIGS. 18A through 18C. The ORF (residues206 to 1000; SEQ ID NO: 222) of the cDNA is indicated by nucleotidetriplets, above which the amino acid sequence (SEQ ID NO: 223) of humanINTERCEPT 400 is listed. FIG. 18D is a hydrophobicity plot of humanINTERCEPT 400 protein. The nucleotide sequence (SEQ ID NO: 241) of acDNA encoding the murine INTERCEPT 400 protein described herein islisted in FIGS. 18E and 18F. The ORF (residues 3 to 524; SEQ ID NO: 242)of the cDNA is indicated by nucleotide triplets, above which the aminoacid sequence (SEQ ID NO: 243) of murine INTERCEPT 400 is listed. FIG.18G is a hydrophobicity plot of murine INTERCEPT 400 protein. Analignment of the amino acid sequences of human INTERCEPT 400 protein(SEQ ID NO: 223) and murine INTERCEPT 400 protein (SEQ ID NO: 243) aminoacid sequences is shown in FIG. 18H. An alignment of the nucleotidesequences of the human (SEQ ID NO: 222) and murine (SEQ ID NO: 242) ORFsencoding INTERCEPT 400 protein is shown in FIGS. 181 through 18K. FIG.18L is an alignment of the amino acid sequences of human INTERCEPT 400protein (“1400”; SEQ ID NO: 223) and murine Cig30 protein (“CIG30”; SEQID NO: 239). An alignment of the nucleotide sequences of the ORFsencoding human INTERCEPT 400 protein (“1400”; SEQ ID NO: 222) and theORF encoding murine Cig30 (“CIG30”; SEQ ID NO: 238) is shown in FIGS.18M through 180. The nucleotide sequence (SEQ ID NO: 251) of a cDNAencoding the rat INTERCEPT 400 protein described herein is listed inFIGS. 18P and 18Q. The ORF (residues 1 to 432; SEQ ID NO: 252) of thecDNA is indicated by nucleotide triplets, above which the amino acidsequence (SEQ ID NO: 253) of rat INTERCEPT 400 is listed. FIG. 18R is analignment of the amino acid sequences of human (SEQ ID NO: 223), murine(SEQ ID NO: 243), and rat (SEQ ID NO: 253) INTERCEPT 400 proteins.

[0099]FIG. 19 comprises FIGS. 19A through 19M. The nucleotide sequence(SEQ ID NO: 271) of a cDNA encoding the human INTERCEPT 217 proteindescribed herein is listed in FIGS. 19A through 19E. The open readingframe (ORF; residues 215 to 1579; SEQ ID NO: 272) of the cDNA isindicated by nucleotide triplets, above which the amino acid sequence(SEQ ID NO: 273) of human INTERCEPT 217 is listed. FIG. 19F is ahydrophobicity plot of human INTERCEPT 217 protein. An alignment of theamino acid sequences of human INTERCEPT 217 protein (“H”; SEQ ID NO:273) and porcine ribonuclease inhibitor protein (“P”; SwissProtAccession number P10775; SEQ ID NO: 334) is shown in FIGS. 19G and 19H.These alignments were made using the ALIGN software {Myers and Miller(1989) CABIOS, ver. 2.0}; pam120.mat scoring matrix; gap openingpenalty=12, gap extension penalty=4). The nucleotide sequence (SEQ IDNO: 362) of an ORF encoding the murine INTERCEPT 217 protein describedherein is listed in FIGS. 191 through 19K. The ORF (residues 1 to 960;SEQ ID NO: 362) is indicated by nucleotide triplets, beneath which theamino acid sequence (SEQ ID NO: 363) of murine INTERCEPT 217 is listed.FIG. 19L is a hydrophobicity plot of murine INTERCEPT 217 protein. Analignment of the amino acid sequences of human INTERCEPT 217 protein(“H”; SEQ ID NO: 273) and murine INTERCEPT 217 protein (“M”; SEQ ID NO:363) is shown in FIG. 1M. These alignments were made using the BESTFITsoftware (BLOSUM62 scoring matrix, gap opening penalty=12, frameshiftgap penalty=5, gap extension penalty=4).

[0100]FIG. 20 comprises FIGS. 20A through 20D. The nucleotide sequence(SEQ ID NO: 279) of a cDNA encoding the human INTERCEPT 297 proteindescribed herein is listed in FIGS. 20A, 20B, and 20C. The open readingframe (ORF; residues 40 to 1152; SEQ ID NO: 280) of the cDNA isindicated by nucleotide triplets, above which the amino acid sequence(SEQ ID NO: 281) of human INTERCEPT 297 is listed. FIG. 20D is ahydrophobicity plot of human INTERCEPT 297 protein.

[0101]FIG. 21 comprises FIGS. 21A through 21R. The nucleotide sequence(SEQ ID NO: 303) of a cDNA encoding the human TANGO 276 proteindescribed herein is listed in FIGS. 21A to 21D. The ORF (residues 58 to786; SEQ ID NO: 304) of the cDNA is indicated by nucleotide triplets,above which the amino acid sequence (SEQ ID NO: 305) of human TANGO 276is listed. FIG. 21E is a hydrophobicity plot of TANGO 276 protein. Analignment of the amino acid sequences of human TANGO 276 protein (“H”;—SEQ ID NO: 305) and murine protein M-Sema-F (“M”; SEQ ID NO: 335) isshown in FIGS. 21F to 21H. In FIGS. 211 through 21R, an alignment of thenucleotide sequences of the cDNA encoding human TANGO 276 protein (“H”;SEQ ID NO: 303) and the nucleotide sequences of the cDNA encoding murineprotein M-Sema-F (“M”; SEQ ID NO: 66) is shown. These alignments weremade using the ALIGN software {Myers and Miller (1989) CABIOS, ver.2.0}; pam120.mat scoring matrix; gap opening penalty=12, gap extensionpenalty=4).

[0102]FIG. 22 comprises FIGS. 22A through 22M. The nucleotide sequence(SEQ ID NO: 308) of a cDNA encoding the human TANGO 292 proteindescribed herein is listed in FIGS. 22A to 22C. The ORF (residues 205 to882; SEQ ID NO: 309) of the cDNA is indicated by nucleotide triplets,beneath which the amino acid sequence (SEQ ID NO: 310) of human TANGO292 is listed. FIG. 22D is a hydrophobicity plot of human TANGO 292protein. The nucleotide sequence (SEQ ID NO: 351) of a cDNA encoding thegerbil TANGO 292 protein described herein is listed in FIGS. 22E to 22H.The ORF (residues 89 to 763; SEQ ID NO: 352) of the cDNA is indicated bynucleotide triplets, below which the amino acid sequence (SEQ ID NO:353) of gerbil TANGO 292 is listed. FIGS. 221 to 22K are an alignment ofthe nucleotide sequences of the ORF encoding human TANGO 292 protein(“H”; SEQ ID NO: 308) and the nucleotide sequence of the ORF encodinggerbil TANGO 292 protein (“G”; SEQ ID NO: 351), made using the ALIGNsoftware {Myers and Miller (1989) CABIOS, ver. 2.0}; pam120.mat scoringmatrix; gap opening penalty=12, gap extension penalty=4). FIG. 22L is analignment of the human (H) and gerbil (G) TANGO 292 amino acidsequences, made using the same software and parameters.

[0103]FIG. 22M is a hydrophobicity plot of gerbil TANGO 292 protein.

[0104]FIG. 23 comprises FIGS. 23A through 23J. The nucleotide sequence(SEQ ID NO: 324) of a cDNA encoding the human TANGO 331 proteindescribed herein is listed in FIGS. 23A, 23B, and 23C. The ORF (residues114 to 1172; SEQ ID NO: 325) of the cDNA is indicated by nucleotidetriplets, above which the amino acid sequence (SEQ ID NO: 326) of humanTANGO 331 is listed. FIG. 23D is a hydrophobicity plot of TANGO 331protein. An alignment of the amino acid sequences of human TANGO 331protein (“H”; SEQ ID NO: 326) and Chinese hamster protein HT (“C”; SEQID NO: 339; GenBank Accession No. U48852) is shown in FIG. 23E. In FIGS.23F through 23J, an alignment of the nucleotide sequences of the cDNAencoding human TANGO 331 protein (“H”; SEQ ID NO: 324) and thenucleotide sequence of the cDNA encoding Chinese hamster protein HT(“C”; SEQ ID NO: 340) is shown. These alignments were made using theALIGN software {Myers and Miller (1989) CABIOS, ver. 2.0}; pam120.matscoring matrix; gap opening penalty=12, gap extension penalty=4).

[0105]FIG. 24 comprises FIGS. 24A through 24U. The nucleotide sequence(SEQ ID NO: 329) of a cDNA encoding the human TANGO 332 proteindescribed herein is listed in FIGS. 24A through 24E. The ORF (residues173 to 2185; SEQ ID NO: 330) of the cDNA is indicated by nucleotidetriplets, above which the amino acid sequence (SEQ ID NO: 331) of humanTANGO 332 protein is listed. FIG. 24F is a hydrophobicity plot of TANGO332 protein. An alignment of the amino acid sequences of TANGO 332protein (“332”; SEQ ID NO: 331) and BEF protein (“BEF”; SEQ ID NO: 341)is shown in FIGS. 24G and 24H. An alignment of the amino acid sequencesof human TANGO 332 protein (“H”; SEQ ID NO: 331) and murine brevidinprotein (“M”; SEQ ID NO: 342) is shown in FIGS. 241 to 24K. In FIGS. 24Lthrough 24U, an alignment of the nucleotide sequences of the cDNAencoding human TANGO 332 protein (“H”; SEQ ID NO: 330) and thenucleotide sequence of the cDNA encoding murine brevidin protein (“M”;SEQ ID NO: 343) is shown. These alignments were made using the ALIGNsoftware {Myers and Miller (1989) CABIOS, ver. 2.0}; pam120.mat scoringmatrix; gap opening penalty=12, gap extension penalty=4).

[0106]FIG. 25 comprises FIGS. 25A to 25M. The nucleotide sequence (SEQID NO: 371) of a cDNA encoding the human TANGO 202 protein describedherein is listed in FIGS. 25A to 25D. The open reading frame (ORF;residues 34 to 1458; SEQ ID NO: 372) of the cDNA is indicated bynucleotide triplets, above which the amino acid sequence (SEQ ID NO:373) of human TANGO 202 is listed. The nucleotide sequence (SEQ ID NO:437) of a cDNA encoding the murine TANGO 202 protein described herein islisted in FIGS. 25E to 251. The ORF (residues 81 to 1490; SEQ ID NO:438) of the cDNA is indicated by nucleotide triplets, above which theamino acid sequence (SEQ ID NO: 439) of murine TANGO 202 is listed. Analignment of the amino acid sequences of human (“Hum.”; SEQ ID NO: 373)and murine (“Mur.”; SEQ ID NO: 439) TANGO 202 protein is shown in FIGS.25J and 25K. FIG. 25L is a hydrophobicity plot of human TANGO 202protein. FIG. 25M is a hydrophobicity plot of murine TANGO 202 protein.

[0107]FIG. 26 comprises FIGS. 26A to 26Q-19. The nucleotide sequence(SEQ ID NO: 379) of a cDNA encoding the human TANGO 234 proteindescribed herein is listed in FIGS. 26A to 261. The ORF (residues 28 to4386; SEQ ID NO: 380) of the cDNA is indicated by nucleotide triplets,above which the amino acid sequence (SEQ ID NO: 381) of human TANGO 234is listed. FIG. 26J is a hydrophobicity plot of human TANGO 234 protein.An alignment of the amino acid sequences of human TANGO 234 (“Hum”; SEQID NO: 381) and bovine WC1 (“WC1”; SEQ ID NO: 448) proteins is shown inFIGS. 26K to 26P. An alignment of the nucleotide sequences of an ORFencoding human TANGO 234 (“Hum”; SEQ ID NO: 380) and an ORF encodingbovine WC1 (“WC1”; SEQ ID NO: 449) proteins is shown in FIGS. 26Q-1 to26Q-19.

[0108]FIG. 27 comprises FIGS. 27A to 27U. The nucleotide sequence (SEQID NO: 387) of a cDNA encoding the human TANGO 265 protein describedherein is listed in FIGS. 27A to 27E. The ORF (residues 32 to 2314; SEQID NO: 388) of the cDNA is indicated by nucleotide triplets, above whichthe amino acid sequence (SEQ ID NO: 389) of human TANGO 265 is listed.An alignment of the amino acid sequences of human TANGO 265 protein(“Hum.”; SEQ ID NO: 389) and murine semaphorin B protein (“Mur.”; SEQ IDNO: 440; GenBank Accession No. X85991) is shown in FIGS. 27F to 27H. InFIGS. 271 to 27T, an alignment of the nucleotide sequences of the cDNAencoding human TANGO 265 protein (“Hum.”; SEQ ID NO: 387) and thenucleotide sequences of the cDNA encoding murine semaphorin B protein(“Mur.”; SEQ ID NO: 441; GenBank Accession No. X85991) is shown. FIG.27U is a hydrophobicity plot of TANGO 265 protein.

[0109]FIG. 28 comprises FIGS. 28A to 281. The nucleotide sequence (SEQID NO: 403) of a cDNA encoding the human TANGO 286 protein describedherein is listed in FIGS. 28A to 28D. The ORF (residues 133 to 1497; SEQID NO: 404) of the cDNA is indicated by nucleotide triplets, above whichthe amino acid sequence (SEQ ID NO: 405) of human TANGO 286 is listed.FIG. 28E is a hydrophobicity plot of TANGO 286 protein. An alignment ofthe amino acid sequences of human TANGO 286 (“286”; SEQ ID NO: 405) andBPI protein (“BPI”. SEQ ID NO: 408) protein is shown in FIGS. 28F and28G. An alignment of the amino acid sequences of human TANGO 286 (“286”;SEQ ID NO: 405) and RENP protein (“RENP”; SEQ ID NO: 409) is shown inFIGS. 28H and 281.

[0110]FIG. 29 comprises FIGS. 29A to 29H. The nucleotide sequence (SEQID NO: 415) of a cDNA encoding the human TANGO 294 protein describedherein is listed in FIGS. 29A to 29C. The ORF (residues 126 to 1394; SEQID NO: 416) of the cDNA is indicated by nucleotide triplets, above whichthe amino acid sequence (SEQ ID NO: 417) of human TANGO 294 is listed.An alignment of the amino acid sequences of human TANGO 294 protein(“294”; SEQ ID NO: 417) and a known human lipase protein (“HLP”; SEQ IDNO: 445; GenBank Accession No. NP_004181) is shown in FIGS. 29D and 29E.FIG. 29F is a hydrophobicity plot of TANGO 294 protein. An alignment ofthe amino acid sequences of human TANGO 294 protein (“294”; SEQ ID NO:417) and a known human lysosomal acid lipase protein (“LAL”; SEQ ID NO:411) is shown in FIGS. 29G and 29H.

[0111]FIG. 30 comprises FIGS. 30A to 30G. The nucleotide sequence (SEQID NO: 423) of a cDNA encoding the human INTERCEPT 296 protein describedherein is listed in FIGS. 30A to 30C. The ORF (residues 70 to 1098; SEQID NO: 424) of the cDNA is indicated by nucleotide triplets, above whichthe amino acid sequence (SEQ ID NO: 425) of human INTERCEPT 296 proteinis listed. FIG. 30D is a hydrophobicity plot of INTERCEPT 296 protein.An alignment of the amino acid sequences of human INTERCEPT 296 protein(“296”; SEQ ID NO: 425) and C. elegans C06E1.3 related protein (“CRP”;SEQ ID NO: 410) is shown in FIGS. 30E through 30G.

DETAILED DESCRIPTION OF THE INVENTION

[0112] The present invention is based, at least in part, on thediscovery of a variety of cDNA molecules which encode proteins which areherein designated TANGO 202, TANGO 210, INTERCEPT 217, TANGO 229, TANGO234, TANGO 265, TANGO 276, TANGO 286, INTERCEPT 289, TANGO 292, TANGO294, INTERCEPT 296, INTERCEPT 297. INTERCEPT 309, TANGO 331, TANGO 332,TANGO 366, INTERCEPT 394, INTERCEPT 400, TANGO 416, MANGO 419, INTERCEPT429, and TANGO 457. These proteins exhibit a variety of physiologicalactivities, and are included in a single application for the sake ofconvenience. It is understood that the allowability or non-allowabilityof claims directed to one of these proteins has no bearing on theallowability of claims directed to the others. The characteristics ofeach of these proteins and the cDNAs encoding them are describedseparately in the ensuing sections. In addition to the full lengthmature and immature proteins described in the following sections, theinvention includes fragments, derivatives, and variants of theseproteins, as described herein. These proteins, fragments, derivatives,and variants are collectively referred to herein as polypeptides of theinvention or proteins of the invention.

[0113] TANGO 416

[0114] Expression of cDNA encoding a TANGO 416 protein was up-regulatedin porcine endothelial cells that were activated using one or more ofbacterial lipopolysaccharide, tumor necrosis factor alpha, and humanserum. Up-regulation was detected by extracting total RNA from activatedcells and subjecting the RNA to reverse transcriptase polymerase chainreaction for differential display. cDNA clones encoding at least aportion of human TANGO 416 protein and corresponding to the porcineTANGO 416 cDNA were isolated from human fetal spleen and osteoblast cDNAlibraries (including a clone designated jthsa97d5 obtained from a fetalspleen library, a clone designated jthoc122e2 obtained from anosteoblast library, and a clone designated jthsa121f10 obtained from afetal spleen library).

[0115] Human TANGO 416 protein is a transmembrane protein which canoccur in at least two alternative forms, which differ in the presence orabsence of a single amino acid residue (i.e. the glutamine residue atamino acid residue 830 of SEQ ID NO: 3 and corresponding nucleotideresidues 2863-2865 in SEQ ID NO: 1). In this application, reference toamino acid and nucleotide residues is made to those residues in thelonger form of TANGO 416 (i.e. the form having the amino acid sequenceSEQ ID NO: 3 and the corresponding cDNA and ORF sequences SEQ ID NOs: 1and 2, respectively).

[0116] The longer form of TANGO 416 has a glutamine residue at aminoacid residue 830 that is not present in the shorter form of TANGO 416.

[0117] It is understood that both forms of TANGO 416 can exhibit thesame biological properties, and that references to amino acid residuesnumbered 831 or higher in SEQ ID NO: 3 correspond to amino acid residueshaving the next lower number in SEQ ID NO: 33 (i.e. amino acid residue901 in the longer form of TANGO 416 {SEQ ID NO: 3} corresponds to aminoacid residue 900 in the shorter form of TANGO 416 {SEQ ID NO: 33}).Similarly, references to nucleotide residues numbered 2866 or higher inSEQ ID NO: 1 correspond to nucleotide residues having a number that islower by 3 in SEQ ID NO: 31 (i.e. nucleotide residue 2903 in the longerform of TANGO 416 {SEQ ID NO: 1} corresponds to nucleotide residue 2900in the shorter form of TANGO 416 {SEQ ID NO: 31}).

[0118] The full length of a cDNA which was isolated from a human fetalspleen cDNA library and which encodes human TANGO 416 protein (FIG. 1;SEQ ID NO: 1; i.e. the longer form of TANGO 416) is 5121 nucleotideresidues. The open reading frame (ORF) of this cDNA, nucleotide residues376 to 3780 of SEQ ID NO: 1 (i.e., SEQ ID NO: 2), encodes a 1135-aminoacid residue protein (FIG. 1; SEQ ID NO: 3), corresponding to a1108-residue transmembrane mature protein.

[0119] The invention thus includes purified human TANGO 416 protein,both in the form of the immature 1135 amino acid residue protein (SEQ IDNO: 3, including the shorter 1134-residue protein {SEQ ID NO: 33}) andin the form of the mature 1108 amino acid residue protein (SEQ ID NO: 5,including the shorter 1107-residue protein {SEQ ID NO: 35}). Maturehuman TANGO 416 proteins can be synthesized without the signal sequencepolypeptide at the amino terminus thereof, or they can be synthesized bygenerating immature TANGO 416 protein and cleaving the signal sequencetherefrom.

[0120] The invention includes nucleic acid molecules which encode apolypeptide of the invention. Such nucleic acids include, for example, aDNA molecule having the nucleotide sequence listed in SEQ ID NOs: 1, 2,31, and 32, such as the portion which encodes a mature TANGO 416protein, an immature TANGO 416 protein, or a domain of a TANGO 416protein. These nucleic acids are among the nucleic acids of theinvention.

[0121] TANGO 416 proteins and nucleic acid molecules encoding themcomprise a family of molecules having certain conserved structural andfunctional features. As used in this disclosure, the term “family” meanstwo or more proteins or nucleic acid molecules having a common orsimilar domain structure and having sufficient amino acid or nucleotidesequence identity as defined herein. Family members can be from eitherthe same or different species (e.g., human and mouse). For example, afamily can comprise two or more proteins of human origin, or cancomprise one or more proteins of human origin and one or more ofnon-human origin.

[0122] A common domain present in TANGO 416 proteins is a signalsequence. As used herein, a signal sequence includes a peptide of atleast about 10 amino acid residues in length which occurs at the aminoterminus of membrane-bound and secreted proteins and which contains atleast about 45% hydrophobic amino acid residues such as alanine,leucine, isoleucine, phenylalanine, proline, tyrosine, tryptophan, orvaline. In one embodiment, a signal sequence contains at least about 10to 35 amino acid residues, and has at least about 35-60%, morepreferably 40-50%, and more preferably at least about 45% hydrophobicresidues. A signal sequence serves to direct a protein containing such asequence to a lipid bi-layer. Thus, in one embodiment, a TANGO 416protein contains a signal sequence corresponding to amino acid residues1 to 27 of SEQ ID NO: 3 and 33 (i.e. SEQ ID NO: 4). It is recognizedthat the carboxyl terminal boundary of the signal sequence can belocated one or two residues from the residue identified above (i.e.,following residues 25, 26, 27, 28, or 29 of SEQ ID NOs: 3 and 33). Thesignal sequence is cleaved during processing of the mature protein.

[0123] TANGO 416 proteins include a transmembrane domain and twoextra-membrane domains flanking the cell membrane. The transmembranedomain corresponds to about amino acid residues 701 to 721 of SEQ IDNOs: 3 and 33 (i.e., the transmembrane domain having the sequence SEQ IDNO: 7). One of the extra-membrane domains corresponds to about aminoacid residues 28 to 700 of SEQ ID NOs: 3 and 33 (i.e. the domain havingthe sequence SEQ ID NO: 6). The other extra-membrane domain correspondsto about amino acid residues 722 to 1135 of SEQ ID NO: 3 (i.e. residues722 to 1134 of SEQ ID NO: 33, this domain having the sequence SEQ ID NO:8 in the longer form of TANGO 416 and SEQ ID NO: 38 in the shorterform). In one embodiment, the extra-membrane domain corresponding to SEQID NO: 6 is an extra-cellular domain and the other extra-membrane domainis an intracellular domain. In an alternative embodiment, theextra-membrane domain corresponding to SEQ ID NO: 6 is an intracellulardomain and the other extra-membrane domain is an extra-cellular domain.

[0124] As used herein, an “extracellular domain” refers to a portion ofa protein which is localized to the non-cytoplasmic side of a lipidbi-layer of a cell when a nucleic acid encoding the protein is expressedin the cell. A “transmembrane domain” refers to an amino acid sequencewhich is at least about 20 to 25 amino acid residues in length and whichcontains at least about 65-70% hydrophobic amino acid residues such asalanine, leucine, phenylalanine, protein, tyrosine, tryptophan, orvaline. As used herein, a “cytoplasmic domain” refers to a portion of aprotein which is localized to the cytoplasmic side of a lipid bi-layerof a cell when a nucleic acid encoding the protein is expressed in thecell.

[0125] TANGO 416 proteins typically comprise a variety of potentialpost-translational modification sites and protein domains (oftenpositioned within an extracellular domain), such as those describedherein in Table 1, as predicted by computerized sequence analysis ofTANGO 416 proteins using amino acid sequence comparison software(comparing the amino acid sequence of TANGO 416 with the information inthe PROSITE database {rel. 12.2; February 1995} and the Hidden MarkovModels database {Rel. PFAM 3.3}). TABLE I Type of Potential ModificationSite Amino Acid Residues Amino or Domain of SEQ ID NO: 3 Acid SequenceN-glycosylation site 103 to 106 NCSI 269 to 272 NATD 420 to 423 NATL 559to 562 NTTV 583 to 586 NNTA 641 to 644 NVSM 766 to 769 NGTL 816 to 819NFSL cAMP/cGMP-dependent 728 to 731 KKDT protein kinase 748 to 751 KRPSphosphorylation site 979 to 982 KKKS Protein kinase C 63 to 65 TVRphosphorylation site 290 to 292 SPK 296 to 298 TFK 301 to 303 SER 447 to449 TVK 552 to 554 SPK 848 to 850 SFR 857 to 859 SYR 869 to 871 SLK 873to 875 SGR 1082 to 1084 SSK Casein kinase II 160 to 163 SAFDphosphorylation site 177 to 180 SAND 188 to 191 TRTD 210 to 213 SSYE 217to 220 TASD 235 to 238 SISD 271 to 274 TDPD 468 to 471 SRYE 488 to 491TATD 503 to 506 TILE 565 to 568 TIID 650 to 653 TEWE 869 to 872 SLKD 883to 886 SDYD 891 to 894 SPID 966 to 969 SLED 990 to 993 SPND 1022 to 1025TYSE 1027 to 1030 SEVD Tyrosine Kinase 187 to 195 RTRTDGAKYPhosphorylation Site 409 to 415 KTYENNY 726 to 734 REKKDTRSY 737 to 743RVAESTY N-myristoylation site 41 to 46 GSVIAR 192 to 197 GAKYAE 481 to486 GAYITT 511 to 516 GSSITT 525 to 530 GAIYAL 593 to 598 GAESGF 623 to628 GNEENI 707 to 712 GAICAV 788 to 793 GQMGSR 851 to 856 GNKYSR 1074 to1079 GTHSSV Cell Attachment Sequence 875 to 877 RGD ZincCarboxypeptidase 639 to 649 HTNVSMDSVPY Zinc-Binding Region 2 SignatureCadherin Extracellular 125 to 135 VEVLDINDNSP Repeated Domain Signature234 to 244 ISISDSNDNSP 342 to 352 IKVVDVNDNKP 453 to 463 VQIINDINDNPP564 to 574 LTIIDENDNVP

[0126] As used herein, the term “post-translational modification site ordomain” refers to a protein region that includes about 3 to 10 aminoacid residues, more preferably about 3 to 6 amino acid residues whereinthe domain has an amino acid sequence which comprises a consensussequence which is recognized and modified by a protein-modifying enzyme.The term also includes protein domains having greater lengths, asindicated herein. Examples of protein-modifying enzymes include aminoacid glycosylases, cAMP- and cGMP-dependent protein kinases, proteinkinase C, casein kinase II, tyrosine kinase, myristoylases, and prenyltransferases. In various embodiments, the protein of the invention hasat least 1, 2, 4, 6, 10, 15, 20, 30, 40, or 50 or more of thepost-translational modification sites described herein in Table I. Inone embodiment, the protein of the invention has all 63 of the sitesdescribed in Table I

[0127] Examples of additional domains present in human TANGO 416 proteininclude cadherin extracellular repeated domains. In one embodiment, theprotein of the invention has at least one domain or signature sequencethat is at least 55%, preferably at least about 65%, 75%, 85%, or 95%identical to one of the cadherin extracellular domains or signaturesequences described herein in Table I. Preferably, the protein of theinvention has 2, 3, 4, or all 5, cadherin extracellular repeateddomains.

[0128] Cadherin extracellular repeated domains have a conservedconsensus sequence that occurs in numerous cadherins. The conservedextracellular cadherin repeated domain sequence, which is frequentlyrepeated in cadherins is {L or I or V}-X-{L or I orV}-X_((1 or 2))-D-X—N-D-{N or H}-X—P, (SEQ ID NO: 450) where X is anyamino acid residue, and wherein the subscript ‘1 or 2’ indicates thateither one or two X residues can be present at that position. Folding ofthe extracellular repeated domain of cadherins is believed to roughlycorrespond to occurrence of extracellular cadherin repeated domains.

[0129] Cadherins are a family of cell-surface proteins which areinvolved in cell-to-cell binding, including specific cell adhesionprocesses which occur during development and adherens junction formationrelated to tissue organization in developing and adult organisms.Cadherins are also involved in intracellular signaling. Repeatedcadherin extracellular domains occur in a variety of cadherins,including, for example, epithelial cadherin (sometimes designatedE-cadherin, uvomorulin, L-CAM, or CDH1), neural cadherin (sometimesdesignated N-cadherin or CDH2), placental cadherin (sometimes designatedP-cadherin or CDH3), retinal cadherin (sometimes designated R-cadherinor CDH4), vascular endothelial cadherin (sometimes designatedVE-cadherin or CDH5), kidney cadherin (sometimes designated K-cadherinor CDH6), cadherin-8 (sometimes designated CDH8), osteoblast cadherin(sometimes designated OB-cadherin or CDH11), brain cadherin (sometimesdesignated BR-cadherin or CDH12), truncated cadherin (sometimesdesignated T-cadherin or CDH13), muscle cadherin (sometimes designatedM-cadherin or CDH14), liver-intestine cadherin (sometimes designatedLI-cadherin), and EP-cadherin. Occurrence of repeated cadherinextracellular domains in TANGO 416 is an indication that TANGO 416 is amember of the cadherin family of proteins, and is thus involved inspecific cell adhesion processes and regulation of intracellularsignaling events in tissues in which it occurs.

[0130] The signal peptide prediction program SIGNALP (Nielsen et al.(1997) Protein Engineering 10:1-6) predicted that human TANGO 416protein includes a 27 amino acid residue signal peptide (amino acidresidues 1 to 27 of SEQ ID NOs: 3 and 33 {SEQ ID NO: 4}) preceding themature TANGO 416 protein (about amino acid residues 28 to 1135 of SEQ IDNO: 3 {SEQ ID NO: 5} and about amino acid residues 28 to 1134 of SEQ IDNO: 33 {SEQ ID NO: 35}). Human TANGO 416 protein includes anextracellular domain (about amino acid residues 28 to 700 of SEQ ID NOs:3 and 33 {SEQ ID NO: 6}), a transmembrane domain (about amino acidresidues 701 to 721 of SEQ ID NOs: 3 and 33 {SEQ ID NO: 7}), and anintracellular domain (about amino acid residues 722 to 1135 of SEQ IDNO: 3 {SEQ ID NO: 8} and about amino acid residues 722 to 1134 of SEQ IDNO: 33 {SEQ ID NO: 38}).

[0131]FIG. 3 depicts a hydrophobicity plot of human TANGO 416 protein.Relatively hydrophobic regions are above the dashed horizontal line, andrelatively hydrophilic regions are below the dashed horizontal line. Thehydrophobic region which corresponds to amino acid residues 1 to 27 ofSEQ ID NOs: 3 and 33 is the signal sequence of human TANGO 416 (SEQ IDNO: 4). As described elsewhere herein, relatively hydrophilic regionsare generally located at or near the surface of a protein, and are morefrequently effective immunogenic epitopes than are relativelyhydrophobic regions. For example, the region of human TANGO 416 proteinfrom about amino acid residue 450 to about amino acid residue 470appears to be located at or near the surface of the protein, while theregion from about amino acid residue 335 to about amino acid residue 345appears not to be located at or near the surface.

[0132] The predicted molecular weight of human TANGO 416 protein withoutmodification and prior to cleavage of the signal sequence is about 126.0kilodaltons. The predicted molecular weight of the mature human TANGO416 protein without modification and after cleavage of the signalsequence is about 122.8 kilodaltons.

[0133] TANGO 416 DNA maps to chromosome 4, between chromosomal markersD4S422 and D4S 1576, as assessed by comparing TANGO 416 sequence with anESTs in a mapping database. Other genes which map to this chromosomalsegment include those encoding endothelin-1 receptor precursor,surfactant protein A, transforming growth factor beta signalingprotein-1 (Bsp-1), and a gene highly similar to Mus musculus hemoglobinzeta chain. Thus, disorders previously attributed to these loci byothers can also be attributable to the chromosomal portion encodingTANGO 416.

[0134] cDNA encoding TANGO 416 protein occurs in cDNA librariesgenerated from human fetal spleen tissue and from human osteoblasts.High homology of TANGO 416 cDNA was observed with expressed sequencetags (ESTs) obtained from EST libraries generated from human fetalheart, human fetal lung, human testis, human pancreas, human prostate,and human B cell tissues, indicating that TANGO 416 protein can beexpressed in these tissues as well.

[0135] Residues 1651-4000 of SEQ ID NO: 1 (the nucleotide sequence ofTANGO 416 cDNA) were aligned (using the ALIGN software with gap lengthpenalty of 12, and a gap penalty of 4) with the nucleotide sequence ofthe human testis cDNA clone DKFZp434B0923 listed in GenBank accessionnumber AL137471. This alignment, shown in FIG. 4, was generated usingthe ALIGN software (using the BLOSUM62 scoring matrix, a gap openingpenalty of 12, a gap extension penalty of 4, and a frameshift gappenalty of 5), and indicated 98.6% identity between the two sequences inthe 2350-residue overlapping portion. The nucleotide sequence (SEQ IDNO: 2) of the ORF encoding TANGO 416 was aligned using the ALIGNsoftware (with gap length penalty of 12, and a gap penalty of 4)) withthe nucleotide sequence of the ORF of a murine protocadherin (GenBank™accession number Y08715; Telo et al., 1998, J.

[0136] Biol. Chem. 273:17565-17572), as shown in FIG. 5. This alignmentwas generated using the ALIGN software (using the BLOSUM62 scoringmatrix, a gap opening penalty of 12, a gap extension penalty of 4, and aframeshift gap penalty of 5), and indicated 55.4% identity between thetwo sequences in the overlapping portion. Alignment of the amino acidsequence of TANGO 416 with the amino acid sequence of the murineprotocadherin, as shown in FIG. 6, indicated 32.8% sequence identity and42.2% sequence similarity. This alignment was generated using the ALIGNsoftware (using the BLOSUM62 scoring matrix, a gap opening penalty of12, a gap extension penalty of 4).

[0137] Uses of TANGO 416 Nucleic Acids,

[0138] Polypeptides, and Modulators Thereof

[0139] TANGO 416 proteins are involved in disorders which affect bothtissues in which they are normally expressed and tissues in which theyare normally not expressed. Based on the observations that cDNAcorresponding to TANGO 416 occurs in human fetal spleen and humanosteoblast cDNA libraries, and that ESTs corresponding to portions ofTANGO 416 can be detected in ESTs prepared from each of human fetalheart, human fetal lung, human testis, human pancreas, human prostate,and human B cell tissues, TANGO 416 protein can be involved in one ormore biological processes which occur in these tissues. In particular,TANGO 416 can be involved in modulating growth, proliferation, survival,differentiation, adhesion, and activity of cells of these tissues.Furthermore, because TANGO 416 likely belongs to the cadherin family ofproteins, it can also be involved in modulating movement of cells (e.g.,T cells and other cells of the immune system) through tissues whichexpress receptors for TANGO 416 (e.g. cells which express one or morecadherin receptors, e.g., cells which express integrin αEβ7).

[0140] Integrin αEP7 (sometimes designated αE/HML-1, αE/human mucosallymphocyte-1 and CD103, and described in international patentapplication publication number W095/22610, published on Aug. 24, 1995)is an integrin protein which is expressed by more than 90% of intestinalepithelial lymphocytes, on 40-50% of intestinal lamina propria Tlymphocytes, and on about 2% of peripheral blood leukocyte. IntegrinαEβ7 is also expressed by T lymphocytes at other mucosal epithelia andon about 40% of T cells obtained by bronchioalveolar lavage. IntegrinαEβ7 is apparently not expressed on B cells. A putative endothelialligand designated E-cadherin binds with integrin αEβ7. Antibodies whichbind specifically with the αE subunit of integrin αEP7 have demonstratedefficacy for treatment of inflammatory bowel disease and for reducingpulmonary inflammation and airway hyper-responsiveness in murine modelsof these disorders. Integrin αEβ7 is believed to have a role in bindingof lymphocytes with endothelial cells and with regulation of tissuelevels of T_(H)1 and T_(H)2 cytokines (e.g. IL-5, IL-13) and eotaxin.The ability of TANGO 416 to bind with integrin αEP7 indicates that TANGO416 protein and other TANGO 416-related molecules can be used tomodulate the physiological activities associated with integrin αEβ7function and to treat disorders to which such physiological activitiescontribute.

[0141] In one embodiment of the invention, TANGO 416-related moleculesare used to modulate interaction of cells which normally expressintegrin αEβ7 (e.g. binding with, movement over, among, or past, oractivation of cellular function by) and cells which normally expressTANGO 416. TANGO 416-related molecules can also be used to modulateproduction, release, or both, of cytokines and eotaxin by cells whichnormally express integrin αEP7. TANGO 416 protein can thus be involvedin disorders which affect epithelial and lymphocytic tissues. Suchdisorders include cell proliferation disorders, disorders associatedwith aberrant epithelial permeability, auto-, hypo-, and hyper-immunedisorders, disorders associated with aberrant binding or adhesion ofcells with other cells, and inflammatory disorders. TANGO 416-relatedmolecules can be used to prognosticate, prevent, diagnose, or treat oneor more such disorders. Examples of these disorders include acute andchronic inflammatory diseases of the bowel, colitis of variousetiologies, gastrointestinal infections, gastritis, gastroesophagealreflux disorder, acute and chronic peritonitis, appendicitis, diarrhea,constipation, gastroenteritis, hemorrhoids, proctitis, chronic and acutebronchitis, asthma, pneumonia, hypersensitivity pneumonitis, allergicdisorders, anemia, leukopenia, thrombocytopenia, lymphoproliferativediseases, transplant rejection, graft-versus-host reactions, allergicreactions, hypersplenism, autoimmune disorders, metastasis of tumortissue, cystic fibrosis, various chronic obstructive pulmonarydisorders, pericarditis, hypogonadism, and testosterone deficiencysyndrome.

[0142] Other disorders which can be treated using TANGO 416 proteins,nucleic acids encoding them, and agents that modulate activity orexpression of either of these include disorders of bone and cartilagetissues (e.g., traumatic and degenerative injuries), disorders of thespleen (e.g., lymphoma and splenomegaly), disorders associated withaberrant processing of blood cells in splenic tissue (e.g., disordersinvolving aberrant macrophage activity), cardiovascular disorders (e.g.,disorders of the cardiac muscle and disorders of blood vessels),disorders involving aberrant association (or non-association) of B and Tlymphocytes with each other and with endothelial tissues (e.g., immunedisorders and inflammatory disorders), pancreatic disorders (e.g.,pancreatitis, pancreatic cysts, pancreatic tumors, diabetes mellitus,and islet cell tumors), and disorders of the prostate (e.g.,inflammatory prostatic diseases, prostatic hyperplasia, and prostatetumors).

[0143] TANGO 416 can interact as a ligand with integrin αEP7, asdiscussed above.

[0144] Integrin αEP7 (also designated human mucosal lymphocyte 1 antigenor CD103) is expressed on more than 90% of intestinal epitheliallymphocytes (IEL), and about 40-50% of intestinal lamina propria Tlymphocytes, but only on about 2% of peripheral blood leukocytes.Integrin αEβ7 is also expressed on T lymphocytes which are present atother mucosal epithelial (e.g. on about 40% of T cells recovered bybronchioalveolar lavage {BAL}). Integrin αEP7 does not appear to beexpressed on B lymphocytes. Transforming growth factor beta 1 (TGF-β1)induces expression of integrin αEP7 on both T lymphocytes and culturedmurine mast cells.

[0145] Antibodies which bind specifically with integrin αEβ7 reducemorbidity and pathological effects associated with experimentallyinduced inflammatory bowel disease (IBD; e.g. using the CD45Rb^(hi)SCIDtransfer model of IBD), transmural colitis, (e.g. using interleukin-2{IL-2} knockout mice immunized using 2,4,6-trinitrophenol), andpulmonary inflammation (e.g. using mice sensitized intraperitoneallywith and challenged with aerosol ovalbumin). In BAL fluids obtained frommice which were sensitized and challenged with ovalbumin and to whichanti-integrin αEP7 were administered, decreased numbers of eosinophilsand leukocytes were detected, and levels of T_(H)2 cytokines (e.g. IL-5and IL-13) and eotaxin were decreased as well. Integrin αEβ7 knockout(i.e. nullizygous) mice exhibited decreased numbers of intestinalepithelial lymphocytes, decreased susceptibility to pulmonaryinflammation, reduced airway hyper-responsiveness, and decreased levelsof T_(H)2 cytokines in BAL fluids. These data indicate that integrinαEβ7 can function as a receptor for guiding lymphocytes (e.g. T cells,mast cells, and eosinophils) to mucosal epithelia and maintaining themat those locations. These data also indicate that integrin αEβ7 canmodulate T_(H)1 and T_(H)2 cytokine levels in tissues which containintegrin αEP7-bearing cells (see international patent applicationpublication number W095/22610, published on Aug. 24, 1995).

[0146] TANGO 416 proteins can bind with integrin αEβ7 and therebymodulate the integrin's physiological effects. In particular, TANGO 416proteins can modulate localization of integrin αEβ7-bearing lymphocytesat tissues which express TANGO 416 (e.g. at mucosal epithelia such asintestinal and pulmonary epithelia) and release and maintenance ofT_(H)1 and T_(H)2 cytokine levels in or near such tissues. Modulation ofcytokine levels by TANGO 416 can, in turn, modulate proliferation,activity, and migration of cells of the immune system, such as areassociated with a variety of inflammatory, auto-immune, hypo-immune, andhyper-immune disorders. TANGO 416 proteins, nucleic acids encoding them,and agents that modulate activity or expression of either of these canthus be used to modulate these processes.

[0147] Disorders that involve proliferation, activity, and migration ofimmune cells in the vicinity of mucosal epithelia include, by way ofexample, acute and chronic inflammatory diseases of the bowel (e.g.inflammatory bowel disease and Crohn's disease), colitis (of variousetiologies), gastrointestinal infections (e.g. formation andperseverance of peptic ulcers), gastritis, gastroesophageal refluxdisorder, acute and chronic peritonitis, appendicitis, diarrhea,constipation, gastroenteritis, hemorrhoids, and proctitis. Suchdisorders also include disorders that involve proliferation, activity,and migration of immune cells in the vicinity of pulmonary mucosalepithelial, such as chronic and acute bronchitis, asthma, pneumonia(e.g. pneumococcal, staphylococcal, streptococcal, klebsiellal,hemophilal, viral, fungal, etc.), hyper-sensitivity pneumonitis, andallergic disorders (e.g. hay fever and the like). TANGO 416 proteins,nucleic acids encoding them, and agents that modulate activity orexpression of either of these can thus be used to prognosticate,diagnose, and treat one or more of these disorders.

[0148] Expression of TANGO 416 in osteoblasts is an indication thatTANGO 416 can have a role in modulating bone formation, marrow celldifferentiation and proliferation, and proliferation, differentiation,function, or some combination of these, of bone and cartilage cells.Examples of disorders which can be prognosticated, diagnosed, andtreated using TANGO 416 proteins, nucleic acids encoding them, andagents that modulate activity or expression of either of these includedisorders of bone and cartilage tissues including bone or cartilageinjuries, such as those attributable to trauma (e.g., bone breakage andcartilage tearing), or to degeneration (e.g., osteoporosis andage-related degradation of cartilage). The compositions can also be usedto treat disorders associated with degeneration of joints, such asarthritis (including rheumatoid arthritis), osteoarthritis, and bonewearing.

[0149] Occurrence of TANGO 416 cDNA in a fetal spleen library is anindication that TANGO 416 proteins, nucleic acids encoding them, andagents that modulate activity or expression of either of these can beused to modulate proliferation, differentiation, function, or somecombination of these, of spleen cells (e.g., cells of the splenicconnective tissue, splenic smooth muscle cells, and endothelial cells ofsplenic blood vessels). These compositions can thus be used to treatdisorders of the spleen, (including both the fetal spleen and the adultspleen). Examples of splenic diseases and disorders include spleniclymphoma and splenomegaly. Occurrence of TANGO 416 in splenic tissuefurther indicates that TANGO 416 proteins, nucleic acids encoding them,and agents that modulate activity or expression of either of these canbe used to modulate proliferation, differentiation, function, or somecombination of these, of blood cells that are processed in splenictissue. These cells include cells which are regenerated or phagocytizedwithin the spleen, including, for example, erythrocytes, B and Tlymphocytes, and macrophages. Examples of these disorders includephagocytotic disorders, such as disorders in which engulfinent ofbacteria and viruses in the bloodstream by macrophages in the spleen isinhibited.

[0150] Occurrence in a fetal heart library of an EST which exhibitshomology with cDNA encoding TANGO 416 indicates that TANGO 416 proteins,nucleic acids encoding them, and agents that modulate activity orexpression of either of these can be used to treat cardiovasculardisorders, including disorders of the heart and disorders of the bloodvessels. Examples of cardiac disorders which can be treated in thismanner include ischemic heart diseases (e.g., angina pectoris,myocardial infarction and its aftermath, coronary artery disease,cardiac arrest, and chronic ischemic heart disease), hypertensive heartdisease, pulmonary heart disease, valvular heart disease (e.g.,rheumatic fever and rheumatic heart disease, endocarditis, mitral valveprolapse, and aortic valve stenosis), congenital heart disease (e.g.,valvular and vascular obstructive lesions, atrial or ventricular septaldefect, and patent ductus arteriosus), cardiac arrhythmia, cardiacinsufficiency, endocarditis, pericardial disease, muscular dystrophy,and myocardial disease (e.g., myocarditis, congestive cardiomyopathy,restrictive cardiomyopathy, and hypertrophic cardiomyopathy). Examplesof vascular disorders which can be treated in this manner includearteriosclerosis, atherosclerosis, hypertension, aberrant or non-desiredangiogenesis, stenosis and restenosis, and smooth muscle proliferationin response to traumatic injury.

[0151] Involvement of TANGO 416 protein in binding of cells is anindication that TANGO 416 can be involved in disorders associated withaberrant binding or adhesion of cells with other cells, withextracellular matrix, or with foreign materials. Disorders involvingaberrant binding or adhesion of cells with other cells include bothdisorders in which cells normally bind with one another (e.g.,metastasis of normally solid tumor tissue cells away from the tumor siteof origin or immune hypersensitivity) and disorders in which the cellsdo not normally bind with one another, but do bind with one another inindividuals afflicted with the disorder (e.g., metastasis of tumor cellsinto a tissue in which the cells do not normally occur, autoimmunedisorders infections, wherein cells with which T cells bind are notnormally present in the animal, or disorders associated with abnormalblood coagulation). Disorders involving aberrant binding or adhesion ofcells with tissue on which TANGO 416 is normally expressed, includethose in which the cells normally do, but aberrantly do not, bind withTANGO 416-expressing tissue as well as those (e.g., metastasis ofcancers cells into mucosal epithelium) in which the cells normally donot bind with TANGO 416-expressing tissue, but aberrantly do. TANGO 416proteins, nucleic acids encoding them, and agents that modulate activityor expression of either of these can be used to prognosticate, diagnose,and treat one or more of these disorders.

[0152] Like many transmembrane signaling proteins, TANGO 416 proteincomprises extracellular domains capable of interacting withenvironmental cues (e.g., the presence or absence of particular cells,proteins, or small molecules) and a cytoplasmic domain having asubstantial size. Numerous cadherins interact with catenins, tyrosinekinases, and other proteins which can influence the structure of theintracellular matrix. TANGO 416 can also interact with such proteins,and the existence of numerous post-translationally modifiable sites (seeTable I) on TANGO 416 is an indication that TANGO 416 can be involved intransducing signals across the cell membrane. Binding of a ligand ofTANGO 416 protein (e.g. integrin αEβ7 on the surface of a different cellsuch as a leukocyte) with a portion of the protein located on one sideof the membrane can affect one or more characteristics (e.g.,conformation, phosphorylation state, or level or specificity ofenzymatic activity) of a portion of the TANGO 416 protein located on theother side. Thus, for example, a compound in the extracellularenvironment of a cell which expresses TANGO 416 can bind with theextracellular domain of the protein, thereby effecting a change in acharacteristic of the intracellular portion of the protein, leading toalteration of the physiology of the cell (e.g., effected by an activityexerted by the intracellular portion of the protein on another componentof the cell). The compound in the extracellular environment can, forexample, be a compound dissolved or suspended in a liquid, a compoundattached to another cell of the same animal, or a compound attached to aforeign cell or virus particle.

[0153] TANGO 416 protein can associate with other signal transductionproteins in the cell membrane, thereby modulating the intracellularactivity of those other proteins. TANGO 416 can also bind with amembrane-bound protein (e.g. integrin αEP7) of another cell, therebymodulating physiological activities associated with signal transductionmediated by that membrane-bound protein. By way of example, signaltransduction events associated with integrin αEP7 include modulation ofTH 1 and T_(H)2 cytokine (and eotaxin) production and release byleukocytes and movement and adherence of leukocytes. TANGO 416 proteinand fragments and variants thereof can modulate such activities. TANGO416 proteins can thus have a role in disorders which involve aberranttransmembrane signal transduction. Examples of signaltransduction-related disorders include cystic fibrosis, various chronicobstructive pulmonary disorders, lymphocyte localization and activationdisorders (e.g. transmural colitis, airway hyper-responsiveness, andvarious allergic disorders), and inflammatory disorders such asinflammatory bowel disease. TANGO 416 proteins, nucleic acids encodingthem, and agents that modulate activity or expression of either of thesecan be used to prognosticate, diagnose, and treat one or more of thesedisorders.

[0154] Occurrence of ESTs which exhibit homology with TANGO 416 nucleicacids in EST libraries generated from tissues which comprise endothelialtissues (e.g. fetal heart tissue and testicular tissue) indicates thatTANGO 416-related molecules can be used to prognosticate, diagnose, andtreat one or more other disorders which afflict endothelial tissues andorgans which contain them. By way of example, the heart is surrounded byan endothelial pericardium which can become inflamed, leading topericarditis and other complications. Similarly, the endothelial liningof blood vessels is known to bind lymphocytes (e.g. during ‘rolling’movement of lymphocytes through the vessel and during extravasation oflymphocytes). Disorders which can affect testicular endothelium includehypogonadism and testosterone deficiency syndrome. Interaction of one ormore TANGO 416-related molecules with cells that modulate interaction ofTANGO 416 with integrin αEβ7 cells can inhibit, prevent, or alleviatesuch disorders. Furthermore, interaction of TANGO 416-related moleculeswith sample material (e.g. blood or tissue) obtained by a patient can beused to diagnose such disorders.

[0155] Homology of an EST obtained from a human B cell EST library witha TANGO 416 nucleic acid is an indication that TANGO 416 can modulatedisorders involving inappropriate interaction of B and T cells. Suchdisorders include hypo-, hyper-, and auto-immune disorders and alsoinclude inflammatory disorders. By modulating interactions of B and Tlymphocytes with each other and with endothelial tissues (and othertissues which can express integrin αEP7, TANGO 416 proteins, nucleicacids encoding them, and agents that modulate activity or expression ofeither of these can also be used to treat immune disorders andinflammatory disorders. By way of example, they can be used to treatautoimmune disorders (e.g., arthritis, graft rejection such as allograftrejection), T cell disorders (e.g., AIDS)), bacterial infection,psoriasis, bacteremia, septicemia, cerebral malaria, inflammatory boweldisease, arthritis (e.g., rheumatoid arthritis, osteoarthritis), andallergic inflammatory disorders (e.g., asthma or psoriasis).

[0156] Homology of an EST of a library made using cDNA obtained frompancreatic tissue with TANGO 416 cDNA sequence indicates that TANGO 416proteins, nucleic acids encoding them, and agents that modulate activityor expression of either of these can be used to treat pancreaticdisorders. Examples of pancreatic disorders which can be treated in thismanner include pancreatitis (e.g., acute hemorrhagic pancreatitis andchronic pancreatitis), pancreatic cysts (e.g., congenital cysts,pseudocysts, and benign or malignant neoplastic cysts), pancreatictumors (e.g., pancreatic carcinoma and adenoma), diabetes mellitus(e.g., insulin- and non-insulin-dependent types, impaired glucosetolerance, and gestational diabetes), and islet cell tumors (e.g.,insulinomas, adenomas, Zollinger-Ellison syndrome, glucagonomas, andsomatostatinoma).

[0157] cDNA encoding TANGO 416 also exhibits homology with an EST of alibrary made using cDNA obtained from prostate tissue. Thus, TANGO 416proteins, nucleic acids encoding them, and agents that modulate activityor expression of either of these can be used to treat prostatedisorders. Examples of prostate disorders which can be treated in thismanner include inflammatory prostatic diseases (e.g., acute and chronicprostatitis and granulomatous prostatitis), prostatic hyperplasia (e.g.,benign prostatic hypertrophy or hyperplasia), and prostate neoplasms andtumors (e.g., carcinomas).

[0158] Homology of TANGO 416 protein with murine vascular endothelialcadherin-2 (mVE-cad-2; Telo et al., 1998, J. Biol. Chem.273:17565-17572; GenBank™ accession number Y08715; sometimes designatedprotocadherin; see FIGS. 5 and 6) is an indication that TANGO 416 is ahuman orthologue of that mVE-cad-2, and exhibits one or more of the sameactivities. That is, TANGO 416 can be involved in adherens junctionformation and maintenance, and can thereby modulate endothelialpermeability to plasma proteins and circulating cells.

[0159] TANGO 457

[0160] The TANGO 457 proteins and nucleic acid molecules comprisefamilies of molecules having certain conserved structural and functionalfeatures.

[0161] For example, the TANGO 457 proteins of the invention can havesignal sequences. In certain embodiments, a TANGO 457 polypeptide caninclude the amino acid sequence SEQ ID NO: 55 at its amino terminus, andthe signal sequence is located at amino acids 1 to 21, 1 to 22, 1 to 23,1 to 24, 1 to 25, 1 to 26, or 1 to 27 of SEQ ID NO: 53. In suchembodiments of the invention, the domains and the mature proteinresulting from cleavage of such signal peptides are also includedherein. For example, the cleavage of a signal sequence consisting ofamino acids 1 to 24 of SEQ ID NO: 53 (SEQ ID NO: 55) results in acytoplasmic domain consisting of amino acids 25 to 264, a transmembranedomain consisting of amino acids 265 to 282, an extracellular domainconsisting of amino acids 283 to 365, of SEQ ID NO: 53 (SEQ ID NO: 56,59, and 60, respectively) and the mature TANGO 457 protein correspondingto amino acids 25 to 365 of SEQ ID NO: 53 (SEQ ID NO: 54). The signalsequence is normally cleaved during processing of the mature protein.

[0162] A TANGO 457 family member can include one or more of thefollowing domains: (1) an extracellular domain; (2) a transmembranedomain; and (3) a cytoplasmic domain. For example, in one embodiment, aTANGO 457 protein contains a cytoplasmic domain at about amino acidresidues 1 to 264 of SEQ ID NO: 53 (SEQ ID NO: 56), a transmembranedomain at about amino acid residues 265 to 282 of SEQ ID NO: 53 (SEQ IDNO: 59), and an extracellular domain at about amino acid residues 283 to365 of SEQ ID NO: 53 (SEQ ID NO: 60). In another embodiment, a humanTANGO 457 protein contains an cytoplasmic domain at amino acid residues283 to 365 of SEQ ID NO: 53 (SEQ ID NO: 60), a transmembrane domain atamino acid residues 265 to 282 of SEQ ID NO: 53 (SEQ ID NO: 59), and anextracellular domain at amino acid residues 1 to 264 of SEQ ID NO: 53(SEQ ID NO: 56).

[0163] A TANGO 457 family member can include one or more TANGO 457 Igdomains. A TANGO 457 Ig domain as described herein is about 68 to 84amino acid residues in length and has the following consensus sequence,beginning about 1 to 15 amino acid residues, more preferably about 3 to10 amino acid residues, and most preferably about 5 amino acid residuesfrom the domain C-terminus: [FYLJ-X—C—X-[VA], wherein [FYL] is aphenylalanine, tyrosine or leucine residue (preferably tyrosine), where“X” is any amino acid, C is a cysteine residue, and [VA] is an alanineresidue or a valine residue. In one embodiment, a TANGO 457 familymember includes one or more Ig domains having an amino acid sequencethat is at least about 55%, preferably at least about 65%, morepreferably at least about 75%, yet more preferably at least about 85%,and most preferably at least about 95% identical to amino acids 41 to124 of SEQ ID NO: 53 (SEQ ID NO: 57). In another embodiment, a TANGO 457family member includes one or more Ig domains having an amino acidsequence that is at least about 55%, preferably at least about 65%, morepreferably at least about 75%, yet more preferably at least about 85%,and most preferably at least about 95% identical to amino acids 163 to230 of SEQ ID NO: 53 (SEQ ID NO: 58).

[0164] In another embodiment, a TANGO 457 family member includes one ormore TANGO 457 Ig domains having an amino acid sequence that is at leastabout 55%, preferably at least about 65%, more preferably at least about75%, yet more preferably at least about 85%, and most preferably atleast about 95% identical to amino acids 41 to 124 and/or 163 to 230 ofSEQ ID NO: 53 (SEQ ID NO: 57 and 58), and has a conserved cysteineresidue about 1 to 15, preferably 1 to 10, more preferably 1 to 8residues downstream from the N-terminus of the Ig domain. Thus, in thisembodiment, amino acids 48 and 163 of SEQ ID NO: 53 are cysteineresidues.

[0165] In another embodiment, a TANGO 457 family member includes one ormore TANGO 457 Ig domains having an amino acid sequence that is at least55%, preferably at least about 65%, more preferably at least about 75%,yet more preferably at least about 85%, and most preferably at leastabout 95% identical to amino acids 41 to 124 and/or 163 to 230 of SEQ IDNO: 53 (SEQ ID NO: 57 and 58), and has a conserved cysteine residueabout 1 to 8 residues downstream from the N-terminus of the TANGO 457 Igdomain, has a conserved cysteine within the consensus sequence thatforms a disulfide with said first conserved cysteine, and has at leastone TANGO 457 biological activity as described herein.

[0166] A cDNA encoding human TANGO 457 was identified by analyzing thesequences of clones present in a human uterine smooth muscle library forsequences that encode wholly secreted or transmembrane proteins. Thisanalysis led to the identification of a clone, jthUa027h12, encodinghuman TANGO 457. The human TANGO 457 cDNA of this clone is 2330nucleotides long (FIG. 7; SEQ ID NO: 51). The open reading frame ofTANGO 457 comprises nucleotides 149 to 1243 of SEQ ID NO: 51 (SEQ ID NO:52), and encodes a transmembrane protein comprising the 365 amino acidsequence depicted in FIG. 7 (SEQ ID NO: 53).

[0167] The signal peptide prediction program SIGNALP (Nielsen et al.(1997) Protein Engineering 10:1-6) predicted that human TANGO 457includes a 24 amino acid signal peptide (amino acids 1 to about aminoacid 24 of SEQ ID NO: 53)(SEQ ID NO: 55) preceding the mature TANGO 457protein (corresponding to about amino acid 25 to amino acid 365 of SEQID NO: 53; SEQ ID NO: 54). Human TANGO 213 is predicted to have amolecular weight of approximately 40.6 kilodaltons prior to cleavage ofits signal peptide and a molecular weight of approximately 38.0kilodaltons subsequent to cleavage of its signal peptide.

[0168] Secretion assays indicate that the polypeptide encoded by humanTANGO 457 is not secreted and thus, likely a transmembrane protein. Thesecretion assays were performed essentially as follows: 8×10 293T cellswere plated per well in a 6-well plate and the cells were incubated ingrowth medium (DMEM, 10% fetal bovine serum, penicillin/streptomycin) at37° C., 5% CO₂ overnight. 293T cells were transfected with 2 microgramsof full-length TANGO 457 inserted in the pMET7 vector/well and 10micrograms LipofectAMINE (GIBCO/BRL Cat. # 18324-012)/well according tothe protocol for GIBCO/BRL LipofectAMINE. The transfectant was removed 5hours later and fresh growth medium was added to allow the cells torecover overnight. The medium was removed and each well was gentlywashed twice with DMEM without methionine and cysteine (ICN Cat. #16-424-54). Next, 1 ml DMEM without methionine and cysteine with 50microcuries of Trans-³⁵S (ICN Cat. # 51006) was added to each well andthe cells were incubated at 37° C., 5% CO₂ for the appropriate timeperiod. A 150 microliters aliquot of conditioned medium was obtained and150 microliters of 2×SDS sample buffer was added to the aliquot. Thesample was heat-inactivated and loaded on a 4-20% SDS-PAGE gel. The gelwas fixed and the presence of secreted protein was detected byautoradiography.

[0169]FIG. 8 depicts a hydrophobicity plot of the human TANGO 457 aminoacid sequence shown in FIG. 7. Relatively hydrophobic regions of theprotein are shown above the horizontal line, and relatively hydrophilicregions of the protein are below the horizontal line. The cysteineresidues (cys) and N-glycosylation site are indicated by short verticallines just below the hydrophobicity trace.

[0170] In one embodiment, a TANGO 457 protein contains a cytoplasmicdomain at about amino acid residues 1 to 264 of SEQ ID NO: 53 (SEQ IDNO: 56), a transmembrane domain at about amino acid residues 265 to 282of SEQ ID NO: 53 (SEQ ID NO: 59), and an extracellular domain at aboutamino acid residues 283 to 365 of SEQ ID NO: 53 (SEQ ID NO: 60). Inanother embodiment, a human TANGO 457 protein contains an cytoplasmicdomain at amino acid residues 283 to 365 of SEQ ID NO: 53 (SEQ ID NO:60), a transmembrane domain at amino acid residues 265 to 282 of SEQ IDNO: 53 (SEQ ID NO: 59), and an extracellular domain at amino acidresidues 1 to 264 of SEQ ID NO: 53 (SEQ ID NO: 56).

[0171] Human TANGO 457 includes an Ig domain at amino acids 41 to 124and 163 to 230 of SEQ ID NO: 53, (SEQ ID NO: 57 and 8).

[0172] Seven N-glycosylation sites are present in TANGO 457. The firsthas the sequence NVTI (at amino acid residues 43 to 46 of SEQ ID NO:53), the second has the sequence NITS (at amino acid residues 57 to 60of SEQ ID NO: 53), the third has the sequence NITW (at amino acidresidues 174 to 177 of SEQ ID NO: 53), the fourth has the sequence NVTS(at amino acid residues 208 to 211 of SEQ ID NO: 53), the fifth has thesequence NSSQ (at amino acid residues 216 to 219 of SEQ ID NO: 53), thesixth has the sequence NFTL (at amino acid residues 242 to 245 of SEQ IDNO: 53), and the seventh has the sequence NFSI (at amino acid residues260 to 263 of SEQ ID NO: 53). TANGO 457 has one glycosaminoglycanattachment site with the sequence SGVG at amino acid residues 331 to 334of SEQ ID NO: 53. Six protein kinase C phosphorylation sites are presentin TANGO 457. The first has the sequence TWR (at amino acid residues 2to 4 of SEQ ID NO: 53), the second has the sequence SLR (at amino acidresidues 106 to 108 of SEQ ID NO: 53), the third has the sequence TQK(at amino acid residues 181 to 183 of SEQ ID NO: 53), the fourth has thesequence TIK (at amino acid residues 199 to 201 of SEQ ID NO: 53), thefifth has the sequence TEK (at amino acid residues 255 to 257 of SEQ IDNO: 53), and the sixth has the sequence SKK (at amino acid residues 301to 303 of SEQ ID NO: 53). TANGO 457 has three casein kinase IIphosphorylation sites. The first has the sequence TEGD (at amino acidresidues 22 to 25 of SEQ ID NO: 53), the second has the sequence SSQE(at amino acid residues 217 to 220 of SEQ ID NO: 53), and the third hasthe sequence SLSE (at amino acid residues 251 to 254 of SEQ ID NO: 53).TANGO 457 has one tyrosine kinase phosphorylation site with the sequenceKENEDKY at amino acid residues 155 to 161 of SEQ ID NO: 53. TwoN-myristoylation sites are present in TANGO 457. The first has thesequence GMKENE (at amino acid residues 153 to 158 of SEQ ID NO: 53) andthe second has the sequence GNVGCV (at amino acid residues 334 to 339 ofSEQ ID NO: 53). Lastly, TANGO 457 has an immunoglobulin and majorhistocompatibility complex protein site with the sequence YQCVVRH atamino acid residues 226 to 232 of SEQ ID NO: 53.

[0173]FIG. 9 depicts a local alignment of the nucleic acid of humanTANGO 457 shown in SEQ ID NO: 51 and a portion of the nucleotidesequence of human chromosome 11p14.3 PAC clone pDJ239b22, from nucleicacids 121077 to 122478 (SEQ ID NO: 61; AC003969). The alignment showsthat there is a 100% nucleotide sequence identity between the TANGO 457sequence of SEQ ID NO: 51 and human chromosome 11p14.3 PAC clonepDJ239b22, over the specified region. Genes known to map to the p14region of human chromosome 11 include those encoding fetal brain protein239 and hepatitis B virus integration site-I (seehttp://www.ncbi.nlm.nih.gov/htbin-post/Omim/getmap?d3076).

[0174] Expressed sequence tags (ESTs) which exhibit homology to TANGO457 (SEQ ID NO: 51) have been isolated from a B-cell leukemia cell lineand from fetal liver, fetal spleen, and placenta tissues. The dbESTaccession numbers of these ESTs are A1361759, AA004711, AA004711, andAI189960, respectively. TANGO 457 (SEQ ID NO: 51) exhibits about 80%homology to A1361759 over about 445 base pairs, from nucleotides 1861 to2306 of TANGO 457. TANGO 457 (SEQ ID NO: 51) exhibits about 77% homologyto AA004711 over about 375 base pairs, from nucleotides 1830 to 2205 ofTANGO 457. TANGO 457 (SEQ ID NO: 51) exhibits about 81% homology toAI189960 over about 415 base pairs, from nucleotides 1908 to 2320.

[0175] Uses of TANGO 457 Nucleic Aids,

[0176] Polypeptides, and Modulators Thereof

[0177] TANGO 457 proteins are involved in disorders which affect bothtissues in which they are normally expressed and tissues in which theyare normally not expressed. Based on the observations that cDNAcorresponding to TANGO 457 occurs in a uterine smooth muscle cDNAlibrary, bears homology to human chromosome 11p14.3 PAC clone pDJ239b22,and bears homology to ESTs isolated from B-cell leukemia, liver, spleen,and placenta libraries, it is evident that TANGO 457 protein is involvedin one or more biological processes which occur in these tissues. Inparticular, TANGO 457 is involved in modulating proliferation,migration, morphology, differentiation, and/or function of cells ofthese tissues. Relevant disorders which involve these tissues arediscussed separately below.

[0178] As TANGO 457 was originally found in a uterine smooth musclelibrary, TANGO 457 polypeptides, nucleic acids, or modulators thereof,can be used to modulate the proliferation, migration, morphology,differentiation, and/or function of cells that form the uterus, e.g.,endometrium endothelial cells and mesometrium smooth muscle cells, andthus to treat uterine disorders such as, e.g., hyperplasia of theendometrium, dysfunctional uterine bleeding (DUB), and uterine cancers(e.g., uterine leiomyomoma, uterine cellular leiomyoma, leiomyosarcomaof the uterus, malignant mixed mullerian tumor of uterus, uterinesarcoma). TANGO 457 polypeptides, nucleic acids, or modulators thereofcan also be used to treat other reproductive disorders, includingovulation disorder, blockage of the fallopian tubes (e.g., due to pelvicinflammatory disease or endometriosis), disorders due to infections(e.g., toxic shock syndrome, chlamydia infection, Herpes infection,human papillomavirus infection), and ovarian disorders (e.g., ovarianendometriosis and ovarian cancers such as ovarian fibroma and ovarianteratoma).

[0179] As TANGO 457 bears homology to regions of human chromosome11p14.3 PAC clone pDJ239b22, and since human chromosome 11p14.3 is thelocation to which such genes as those encoding fetal brain protein 239and hepatitis B virus integration site-I are known to map, TANGO 457nucleic acids, proteins, and modulators thereof can be used to modulateor treat disorders associated with hepatitis B infection (e.g.,hepatitis, e.g., hepatitis B, and hepatocellular carcinomas) as well asCNS related disorders. Such CNS related disorders include but are notlimited to bacterial and viral meningitis, Alzheimer's Disease,Huntington's disease, cerebral toxoplasmosis, Parkinson's disease,multiple sclerosis, brain cancers (e.g., cancers that have metastasizedfrom other tissues (e.g., metastatic carcinoma of the brain), cancers ofthe supportive tissue of the brain (e.g., the glia; including cancerssuch as glioblastoma and astrocytoma), and cancers of other neuraltissues (e.g., acoustic neuroma)), hydrocephalus, and encephalitis.

[0180] TANGO 457 is also expressed in the fetal liver, TANGO 457 nucleicacids, proteins, and modulators thereof can be used to modulate theproliferation, migration, morphology, differentiation, and/or functionof cells that form the liver, e.g., hepatocytes, and thus to treathepatic (liver) disorders, such as jaundice, hepatic failure, hereditaryhyperbiliruinemias (e.g., Gilbert's syndrome, Crigler-Naijar syndromesand Dubin-Johnson and Rotor's syndromes), hepatic circulatory disorders(e.g., hepatic vein thrombosis and portal vein obstruction andthrombosis), hepatitis (e.g., chronic active hepatitis, acute viralhepatitis, and toxic and drug-induced hepatitis), hepatic adverse drugreactions such as hepatotoxicity, fibrosis, cirrhosis (e.g., alcoholiccirrhosis, biliary cirrhosis, and hemochromatosis), and hepaticneoplasms and tumors (e.g., primary carcinoma, hepatoblastoma, andangiosarcoma).

[0181] In addition, TANGO 457 is expressed in the fetal spleen. TANGO457 nucleic acids, proteins, and modulators thereof can be used tomodulate proliferation, migration, morphology, differentiation,function, or some combination of these, of cells that form the spleen,(e.g., cells of the splenic connective tissue, splenic smooth musclecells, or endothelial cells of the splenic blood vessels) or of bloodcells that are processed (e.g., regenerated, matured, or phagocytized)within the spleen, as described elsewhere in this disclosure.

[0182] As both fetal spleen and fetal liver are sites of hematopoiesis,TANGO 457 nucleic acids, proteins, and modulators thereof can also beused to modulate the proliferation, migration, morphology,differentiation, and/or function of hematopoietic cells, e.g.,pluripotential stem cells (e.g., lymphoid cells and myeloid cells), andcan be used to treat hematological disorders.

[0183] Hematological disorders include, but are not limited to,disorders associated with abnormal differentiation or hematopoiesis,morphology, migration, proliferation, or function of blood cellsderived, for example, from myeloid multipotential cells in bone marrow,such as megakaryocytes (and ultimately platelets), monocytes,erythrocytes, and granulocytes (e.g., neutrophils, eosinophils, andbasophils) and from lymphoid multipotential cells, such as T and Blymphocytes.

[0184] Platelet associated disorders include, but are not limited to,thrombocytopenia due to a reduced number of megakaryocytes in the bonemarrow, for example, as a result of chemotherapy; invasive disorders,such as leukemia, idiopathic or drug- or toxin-induced aplasia of themarrow, or rare hereditary amegakaryocytic thrombocytopenias;ineffective thrombopoiesis, for example, as a result of megaloblasticanemia, alcohol toxicity, vitamin B 12 or folate deficiency,myelodysplastic disorders, or rare hereditary disorders (e.g.,Wiskott-Aldrich syndrome and May-hegglin anomaly); a reduction inplatelet distribution, for example, as a result of cirrhosis, a splenicinvasive disease (e.g., Gaucher's disease), or myelofibrosis withextramedullary myeloid metaplasia; increased platelet destruction, forexample, as a result of removal of IgG-coated platelets by themononuclear phagocytic system (e.g., idiopathic thrombocytopenic purpura(ITP), secondary immune thrombocytopenia (e.g., systemic lupuserythematosus, lymphoma, or chronic lymphocytic leukemia), drug-relatedimmune thrombocytopenias (e.g., as with quinidine, aspirin, andheparin), post-transfusion purpura, and neonatal thrombocytopenia as aresult of maternal platelet autoantibodies or maternal plateletalloantibodies). Also included are thrombocytopenia secondary tointravascular clotting and thrombin induced damage to platelets as aresult of, for example, obstetric complications, metastatic tumors,severe gram-negative bacteremia, thrombotic thrombocytopenic purpura, orsevere illness. Also included is dilutional thrombocytopenia, forexample, due to massive hemorrhage. Platelet associated disorders alsoinclude, but are not limited to, essential thrombocytosis andthrombocytosis associated with, for example, splenectomy, acute orchronic inflammatory diseases, hemolytic anemia, carcinoma, Hodgkin'sdisease, lymphoproliferative disorders, and malignant lymphomas.

[0185] Erythrocyte associated disorders include anemias such as, forexample, hemolytic anemias due to hereditary cell membraneabnormalities, such as hereditary spherocytosis, hereditaryelliptocytosis, and hereditary pyropoikilocytosis; hemolytic anemias dueto acquired cell membrane defects, such as paroxysmal nocturnalhemoglobinuria and spur cell anemia; hemolytic anemias caused byantibody reactions, for example to the RBC antigens, or antigens of theABO system, Lewis system, Ii system, Rh system, Kidd system, Duffysystem, and Kell system; methemoglobinemia; a failure of erythropoiesis,for example, as a result of aplastic anemia, pure red cell aplasia,myelodysplastic syndromes, sideroblastic anemias, and congenitaldyserythropoietic anemia; secondary anemia in non-hematolic disorders,for example, as a result of chemotherapy, alcoholism, or liver disease;anemia of chronic disease, such as chronic renal failure; and endocrinedeficiency diseases.

[0186] Other erythrocyte associated disorders include polycythemias suchas, for example, polycythemia vera, secondary polycythemia, and relativepolycythemia.

[0187] Neutrophil associated disorders include neutropenias that resultfrom or accompany a number of conditions, including, but not limited to,chemotherapy; chronic idiopathic neutropenia; Felty's syndrome, acuteinfectious disease, lymphoma or aleukemic lymphocytic leukemia,myelodysplastic syndrome, and rheumatic diseases such as systemic lupuserythematosus, rheumatoid arthritis, and polymyositis. Also included isneutrophilia, for example, accompanying chronic myelogenous leukemia.

[0188] Other hematological disorders include disorders associated withabnormal monocyte and/or macrophage function, such as impairedphagocytosis, chemotaxis, or secretion of cytokines, growth factors andacute-phase reactants, resulting from certain diseases, e.g., lysosomalstorage diseases (e.g., Gaucher's disease); impaired monocyte cytokineproduction, for example, found in some patients with disseminatednon-tuberculous mycobacterial infection who are not infected with HIV;leukocyte adhesion deficiency (LAD), hyperimmunoglobulin E-recurrentinfection (HIE) or Job's syndrome, Chédiak-Higashi syndrome (CHS), andchronic granulomatous diseases (CGD), certain autoimmune diseases, suchas systemic lupus erythematosus and other autoimmune diseasescharacterized by tissue deposition of immune complexes, as seen inSjogren's syndrome, mixed cryoglobulinemia, dermatitis herpetiformis,and chronic progressive multiple sclerosis. Also included are disordersor infections that impair mononuclear phagocyte function, for example,influenza virus infection and AIDS.

[0189] Monocyte associated disorders include monocytoses such as, forexample, monocytoses associated with certain infections such astuberculosis, brucellosis, subacute bacterial endocarditis, RockyMountain spotted fever, malaria, and visceral leishmaniasis (kala azar),in malignancies, leukemias, myeloproliferative syndromes, hemolyticanemias, chronic idiopathic neutropenias, and granulomatous diseasessuch as sarcoidosis, regional enteritis, and some collagen vasculardiseases.

[0190] Other monocyte associated disorders include monocytopenias suchas, for example, monocytopenias that can occur with acute infections,with stress, following administration of glucocorticoids, aplasticanemia, hairy cell leukemia, and acute myelogenous leukemia and as adirect result of administration of myelotoxic and immunosuppressivedrugs.

[0191] Eosinophil associated disorders include eosinphilias such as, forexample, eosinphilias that result from or accompany conditions such asallergic disorders, infections caused by parasites and other organisms,dermatologic diseases, pulmonary diseases, collagen vascular disease,neoplasms, immunodeficiency diseases, gastroenteritis, inflammatorybowel disease, chronic active hepatitis, pancreatitis, andhypopituitarism. Also included are hypereosinophilic syndrome (HES) andchronic and acute eosinophilic leukemias.

[0192] Other eosinophil associated disorders include eosinopenias suchas, for example, eosinopenias that occur with stress, such as acutebacterial infection, and following administration of glucocorticoids.

[0193] Basophil associated disorders include basophilias such as, forexample, basophilias seen in myeloproliferative disorders (e.g., chronicmyeloid leukemia, polycythemia vera, and myeloid metaplasia), followingsplenectomy, hemolytic anemia, ulcerative colitis, varicella infection,and Hodgkin's disease.

[0194] As TANGO 457 is expressed in the placenta, TANGO 457 nucleicacids, proteins, and modulators thereof can be used to modulate theproliferation, migration, morphology, differentiation, and/or functionof cells that form the placenta, e.g., the decidual cells (which ariseduring pregnancy), and thus can be used to treat placental disorders,such as toxemia of pregnancy (e.g., preeclampsia and eclampsia),placentitis, or spontaneous abortion.

[0195] As TANGO 457 is expressed in B-cell, chronic lymphotic leukemia,TANGO 457 nucleic acids, proteins, and modulators thereof can be used tomodulate the proliferation, migration, morphology, differentiation,and/or function of immune cells, e.g. B-cells, dendritic cells, naturalkiller cells and monocytes. TANGO 457 nucleic acids, proteins andmodulators thereof can also be utilized to modulate immunoglobulins andformation of antibodies, and immune-related processes, e.g., the hostimmune response.

[0196] Such TANGO 457 compositions and modulators thereof can beutilized modulate or treat immune disorders that include, but are notlimited to, immune proliferative disorders (e.g., carcinoma, lymphoma,e.g., follicular lymphoma), disorders associated with fightingpathogenic infections (e.g., bacterial, such as chlamydial, infection,parasitic infection, and viral infections such as HSV or HIVinfections), pathogenic disorders associated with immune disorders(e.g., immunodeficiency disorders, such as HIV), autoimmune disorders(e.g., rheumatoid and juvenile arthritis, rheumatism, systemic lupuserythamatosus, graft or allograft rejection, multiple sclerosis, Grave'sdisease, and Hashimoto's disease), immunodeficiency disorders (e.g., Band T cell immunodeficiency disorders and AIDS), bacterial, viral, andparasitic infections (e.g., sepsis, influenza, common colds, hepatitis,HIV infection, malaria, and gonorrhea), disorders associated withundesirable immune reactions with foreign material (e.g., transplantrejection, environmental {e.g., latex} hypersensitivity disorders, andallergic disorders), phagocytic dysfunction disorders (e.g., neutropeniaand chronic granulomatous disease), anaphylaxis, urticaria, andinflammatory disorders (e.g., septicemia, cerebral malaria, inflammatorybowel disease, arthritis such as rheumatoid arthritis andosteoarthritis, allergic inflammatory disorders such as asthma andpsoriasis, apoptotic disorders such as rheumatoid arthritis, systemiclupus erythematosus, and insulin-dependent diabetes mellitus, cytotoxicdisorders, septic shock, and cachexia).

[0197] As TANGO 457 contains one or more Ig domains, and asimmunoglobulin superfamily proteins are cell surface molecules involvedin signal transduction and cellular proliferation, TANGO 457 nucleicacids, proteins and modulators thereof can be utilized to modulate thedevelopment and progression of cancerous and non-cancerous cellproliferative disorders, such as deregulated proliferation (such ashyperdysplasia, hyper-IgM syndrome, or lymphoproliferative disorders),cirrhosis of the liver (a condition in which scarring has overtakennormal liver regeneration processes), treatment of keloid (hypertrophicscar) formation (disfiguring of the skin in which the scarring processinterferes with normal renewal), psoriasis (a common skin conditioncharacterized by excessive proliferation of the skin and delay in propercell fate determination), benign tumors, fibrocystic conditions, andtissue hypertrophy (e.g., prostatic hyperplasia), cancers such asneoplasms or tumors (such as carcinomas, sarcomas, adenomas or myeloidlymphoma tumors, e.g., fibrosarcoma, myxosarcoma, liposarcoma,chondrosarcoma, osteogenic sarcoma, chordoma, angiosarcoma,endotheliosarcoma, lymphangiosarcoma, lymphangioendotheliosarcoma,synovioma, mesothelioma, Ewing's tumor, leimyosarcoma,rhabdotheliosarcoma, colon sarcoma, pancreatic cancer, breast cancer,ovarian cancer, prostate cancer, squamous cell carcinoma, basal cellcarcinoma, adenocarcinoma, sweat gland carcinoma, sebaceous glandcarcinoma, papillary carcinoma, papillary adenocarcinomas,cystadenocarcinoma, medullary carcinoma, bronchogenic carcinoma, renalcell carcinoma, hematoma, bile duct carcinoma, melanoma,choriocarcinoma, semicoma, embryonal carcinoma, Wilms' tumor, cervicalcancer, testicular tumor, lung carcinoma, small cell carcinoma, bladdercarcinoma, epithelial carcinoma, glioma, astrocytoma, medulloblastoma,craniopharyngioma, ependynoma, pinealoma, hemangioblastoma,retinoblastoma), leukemias, (e.g. acute lymphocytic leukemia), acutemyelocytic leukemia (myelolastic, promyelocytic, myelomonocytic,monocytic and erythroleukemia), chronic leukemias (chronic myelocytic(granulocytic) leukemia and chronic lymphocytic leukemia), orpolycythemia vera, or lymphomas (Hodgkin's disease and non-Hodgkin'sdiseases), multiple myelomas and Waldenstrom's macroglobulinemia.

[0198] TANGO 229

[0199] A cDNA clone (designated jthtc001c06) encoding at least a portionof human TANGO 229 protein was isolated from a human T cell cDNAlibrary. Human TANGO 229 protein is a transmembrane protein.

[0200] The full length of the cDNA encoding human TANGO 229 protein(FIG. 10; SEQ ID NO: 71) is 3594 nucleotide residues. The open readingframe (ORF) of this cDNA, nucleotide residues 72 to 2216 of SEQ ID NO:71 (i.e., SEQ ID NO: 72), encodes a 715-amino acid residue protein (FIG.10; SEQ ID NO: 73), corresponding to a 681-residue transmembrane matureprotein.

[0201] The invention thus includes purified human TANGO 229 protein,both in the form of the immature 715 amino acid residue protein (SEQ IDNO: 73) and in the form of the mature 681 amino acid residue protein(SEQ ID NO: 75). Mature human TANGO 229 proteins can be synthesizedwithout the signal sequence polypeptide at the amino terminus thereof,or they can be synthesized by generating immature TANGO 229 protein andcleaving the signal sequence therefrom.

[0202] The invention includes nucleic acid molecules which encode apolypeptide of the invention. Such nucleic acids include, for example, aDNA molecule having the nucleotide sequence listed in SEQ ID NO: 71,such as the portion which encodes mature TANGO 229 protein, immatureTANGO 229 protein, or a domain of TANGO 229 protein. These nucleic acidsare collectively referred to as nucleic acids of the invention.

[0203] TANGO 229 proteins and nucleic acid molecules encoding themcomprise a family of molecules having certain conserved structural andfunctional features.

[0204] A common domain present in TANGO 229 proteins is a signalsequence. In one embodiment, a TANGO 229 protein contains a signalsequence corresponding to amino acid residues 1 to 34 of SEQ ID NO: 73(SEQ ID NO: 74). It is recognized that the carboxyl terminal boundary ofthe signal sequence can be located one or two residues from the residueidentified above (i.e., following residues 32, 33, 34, 35, or 36 of SEQID NO: 73). The signal sequence is cleaved during processing of themature protein.

[0205] TANGO 229 proteins include a transmembrane domain and twoextra-membrane domains flanking the cell membrane. The transmembranedomain corresponds to about amino acid residues 456 to 480 of SEQ ID NO:73 (i.e., the transmembrane domain having the sequence SEQ ID NO: 77).One of the extra-membrane domains corresponds to about amino acidresidues 35 to 455 of SEQ ID NO: 73. This domain has the sequence SEQ IDNO: 76, and is most likely an extracellular domain. The otherextra-membrane domain corresponds to about amino acid residues 481 to715 of SEQ ID NO: 73. This domain has the sequence SEQ ID NO: 78, and ismost likely a cytoplasmic domain. In one embodiment, the domaincorresponding to about amino acid residues 35 to 455 of SEQ ID NO: 73 isa cytoplasmic domain, and the domain corresponding to about amino acidresidues 481 to 715 is an extracellular domain.

[0206] TANGO 229 proteins typically comprise a variety of potentialpost-translational modification sites and protein domains (oftenpositioned within an extracellular domain), such as those describedherein in Table II, as predicted by computerized sequence analysis ofTANGO 229 proteins using amino acid sequence comparison software(comparing the amino acid sequence of TANGO 229 with the information inthe PROSITE database {rel. 12.2; February 1995} and the Hidden MarkovModels database {Rel. PFAM 3.3}). TABLE II Amino Type of PotentialModification Site Acid Residues Amino Acid or Domain of SEQ ID NO: 73Sequence N-glycosylation site 64 to 67 NHTV 124 to 127 NTSE 277 to 280NESG 351 to 354 NNSK 418 to 421 NDSL 455 to 458 NITT 707 to 710 NQTAcAMP/cGMP-dependent protein 322 to 325 KKIT kinase phosphorylation site424 to 427 RKTS 485 to 488 KKGS 553 to 556 RKGS Protein kinase Cphosphorylation site 54 to 56 TSK 129 to 131 TVR 139 to 141 SGR 244 to246 SDK 357 to 359 TYK 433 to 435 STK 527 to 529 TQK 552 to 554 TRK 557to 559 TFR 683 to 685 SQK Casein kinase II phosphorylation site 46 to 49TYQD 66 to 69 TVCE 103 to 106 SSSD 157 to 160 TCLE 226 to 229 SRYE 242to 245 SLSD 275 to 278 SVNE 434 to 437 TKKE 563 to 566 TDAEN-myristoylation site 4 to 9 GARGGG 51 to 56 GTMTSK 60 to 65 GTYPNH 135to 140 GSHISG 214 to 219 GGQISV 230 to 235 GILANG 254 to 259 GCSRSL 265to 270 GQIRAS 326 to 331 GIRTTG 360 to 365 GIVNNE 411 to 416 GCQITQ 453to 458 GINITT 475 to 480 GIFAAF 487 to 492 GSPYGS 646 to 651 GAQDGD 691to 696 GTSDSY Amidation site 76 to 79 KGKR CUB domain  41 to 147 SeeFIG. 10 Factor V/VIII discoidin domain 258 to 409 See FIG. 10

[0207] In various embodiments, the protein of the invention has at least1, 2, 4, 6, 10, 15, or 20 or more of the post-translational modificationsites described herein in Table II.

[0208] Examples of additional domains present in human TANGO 229 proteininclude a CUB domain and a Factor V/VIII discoidin domain. In oneembodiment, the protein of the invention has at least one domain orsignature sequence that is at least 55%, preferably at least about 65%,75%, 85%, or 95% identical to one of the domains or signature sequencesdescribed herein in Table II. Preferably, the protein of the inventionhas at least one CUB domain and one Factor V/VIII discoidin domain.

[0209] CUB domains are extracellular domains of about 110 amino acidresidues which occur in functionally diverse, mostly developmentallyregulated proteins (Bork and Beckmann (1993) J. Mol. Biol. 231:539-545;Bork (1991) FEBS Lett. 282:9-12). Many CUB domains contain fourconserved cysteine residues, although some, like that of TANGO 202,contain only two of the conserved cysteine residues. The structure ofthe CUB domain has been predicted to assume a beta-barrel configuration,similar to that of immunoglobulins. Other proteins which comprise one ormore CUB domains include, for example, mammalian complementsub-components Cls and Clr, hamster serine protease Casp, mammaliancomplement activating component of Ra-reactive factor, vertebrateenteropeptidase, vertebrate bone morphogenic protein 1, sea urchinblastula proteins BP 10 and SpAN, Caenorhabditis elegans hypotheticalproteins F42A10.8 and R151.5, neuropilin (A5 antigen, in which a pair ofFactor V/VIII discoidin domains also occur), sea urchin fibropellins Iand III, mammalian hyaluronate-binding protein TSG-6 (PS4), mammalianspermadhesins, and Xenopus embryonic protein UVS.2. The presence of aCUB domain in TANGO 229 protein indicates that TANGO 229 is involved inone or more physiological processes in which these other CUBdomain-containing proteins are involved, has a biological activity incommon with one or more of these other CUB domain-containing proteins,or both. The presence of a CUB domain in TANGO 229 protein alsoindicates that TANGO 229 can be developmentally regulated.

[0210] Factor V/VIII discoidin domains are involved in binding with cellsurface-attached carbohydrates. These domains occur in a variety ofintracellular, extracellular, and transmembrane proteins, includinghuman and murine coagulation factor V, human and murine coagulationfactor VIII precursor, human and murine neuropilins, a variety ofreceptor-like tyrosine kinases (e.g., neurotrophic tyrosine kinases andcell adhesion tyrosine kinases), carboxypeptidases andcarboxypeptidase-like proteins, milk fat globule glycoproteins, humanbreast epithelial antigen BA46, murine neurexin IV, human X-linkedjuvenile retinoschisis precursor protein, and human contactin associatedprotein. Presence of a Factor V/VIII discoidin domain in TANGO 229indicates that this protein is involved in one or more physiologicalprocesses in which these other Factor V/VIII discoidin domain-containingproteins are involved, has biological activity in common with one ormore of these other Factor V/VIII discoidin domain-containing proteins,or both. Presence of a Factor V/VIII discoidin domain in TANGO 229protein is an indication that TANGO 229 is associated with binding ofone or more glycosylated proteins at the surface of cells which expressTANGO 229. Binding of glycosylated proteins at the cell surface isassociated with several physiologically relevant phenomena, includingcell adhesion (including cell repulsion), transmembrane signaltransduction, and nutrient binding and uptake by cells. The FactorV/VIII discoidin domain of human coagulation factor VIII protein isknown to be involved in binding of factor VIII with von Willebrandfactor and with membrane-associated lipids such as phosphatidylserine.Presence of a Factor V/VIII discoidin domain in TANGO 229 protein isthus an indication that the extracellular portion of TANGO 229 proteincan interact with membrane lipids.

[0211] The signal peptide prediction program SIGNALP (Nielsen et al.(1997) Protein Engineering 10:1-6) predicted that human TANGO 229protein includes a 34 amino acid residue signal peptide (amino acidresidues 1 to 34 of SEQ ID NO: 73; SEQ ID NO: 74) preceding the matureTANGO 229 protein (amino acid residues 35 to 715 of SEQ ID NO: 73; SEQID NO: 75). Human TANGO 229 protein includes an extracellular domain(amino acid residues 35 to 455 of SEQ ID NO: 73; SEQ ID NO: 76), atransmembrane domain (amino acid residues 456 to 480 of SEQ ID NO: 73;SEQ ID NO: 77), and an intracellular domain (amino acid residues 481 to715 of SEQ ID NO: 73; SEQ ID NO: 78). In an alternative embodiment,amino acid residues 35 to 455 of SEQ ID NO: 73 correspond to anintracellular domain of human TANGO 229 protein and residues 481 to 715correspond to an extracellular domain.

[0212]FIG. 10G depicts a hydrophobicity plot of human TANGO 229 protein.

[0213] Relatively hydrophobic regions are above the dashed horizontalline, and relatively hydrophilic regions are below the dashed horizontalline. The hydrophobic region which corresponds to amino acid residues 1to 34 of SEQ ID NO: 73 is the signal sequence of human TANGO 229 (SEQ IDNO: 74). As described elsewhere herein, relatively hydrophilic regionsare generally located at or near the surface of a protein, and are morefrequently effective immunogenic epitopes than are relativelyhydrophobic regions. For example, the region of human TANGO 229 proteinfrom about amino acid residue 50 to about amino acid residue 70 appearsto be located at or near the surface of the protein, while the regionfrom about amino acid residue 195 to about amino acid residue 210appears not to be located at or near the surface.

[0214] The predicted molecular weight of human TANGO 229 protein withoutmodification and prior to cleavage of the signal sequence is about 77.9kilodaltons. The predicted molecular weight of the mature human TANGO229 protein without modification and after cleavage of the signalsequence is about 72.3 kilodaltons.

[0215] Northern hybridization experiments using human tissue samplesindicated that mRNA corresponding to cDNA encoding TANGO 229 isexpressed in the tissues listed in Table 111A, wherein “++” indicatesstrongly detectable expression, “+” indicates a lesser degree ofexpression, and “+/−” indicates a still lesser degree of expression. Inthese tissues, two alternatively spliced forms of cDNA encoding TANGO229 (having sizes of about 2.0 and 4.0 kilobases) were detected. TABLEIIIA Tissue Expression Heart ++ Liver ++ Pancreas ++ Placenta + Brain+/− Lung +/− Skeletal Muscle +/− Kidney +/−

[0216] Northern hybridization experiments using human immune systemtissue samples indicated that mRNA corresponding to the cDNA encodingTANGO 229 is expressed in the tissues listed in Table IIIB. In thesetissues, two alternatively spliced forms of cDNA encoding TANGO 229(having sizes of about 2.0 and 4.9 kilobases) were detected. TABLE IIIBTissue Expression Spleen ++ Lymph node ++ Fetal Liver ++ Peripheralblood leukocytes + Bone Marrow + Thymus +/−

[0217] The nucleotide sequence (SEQ ID NO: 71) of TANGO 229 cDNA wasaligned (using the LALIGN software {Huang and Miller (1991) Adv. Appl.Math. 12:373-381}; pam120 scoring matrix, gap opening penalty=12, gapextension penalty=4) with the nucleotide sequence of the portion ofhuman chromosome region 6q21 listed in GenBank Accession No. Z85999.This alignment indicated 45.8% identity between the two sequences in the3826-residue overlapping portion.

[0218] The nucleotide sequence (SEQ ID NO: 71) of TANGO 229 cDNA wasalso aligned (using the LALIGN software; pam120 scoring matrix, gapopening penalty=12, gap extension penalty=4) with an expressed sequencetag (EST) clone designated BP481 in P.C.T. Publication No. W098/45435.This alignment indicated 72.9% identity between the two sequences in the414-residue overlapping portion.

[0219] Uses of TANGO 229 Nucleic Acids,

[0220] Polypeptides, and Modulators Thereof

[0221] TANGO 229 proteins are involved in disorders which affect bothtissues in which they are normally expressed and tissues in which theyare normally not expressed. Based on the observations that cDNAcorresponding to TANGO 229 occurs in a human T cell cDNA library, andthat RNA corresponding to TANGO 229 is detectable by Northern analysisof human heart, liver, pancreas, placenta, brain lung, skeletal muscle,kidney, spleen, lymph node, peripheral blood leukocyte, bone marrow, andthymus tissues, it is evident that TANGO 229 protein can be involved inone or more biological processes which occur in these tissues. Inparticular, TANGO 229 can be involved in modulating growth,proliferation, survival, differentiation, and activity of cells of thesetissues (e.g., T cells and other cells of the immune system).

[0222] Expression of TANGO 229 in a variety of immune system tissues(e.g., T cells, peripheral blood leukocyte, and spleen, lymph node, bonemarrow, and thymus tissues) is an indication that TANGO 229 can have arole in both normal immune processes and in a variety of disorders whichaffect or involve the immune system, such as the immune disordersdescribed elsewhere in this disclosure.

[0223] The presence of a factor V/VIII discoidin domain in TANGO 229protein is an indication that the protein can be involved in mediatingcell binding and adhesion, including binding/adhesion of cells withother cells, with extracellular matrix, and with foreign materials(i.e., materials not originating in the body of the same individual).Cell binding and adhesion affected by TANGO 229 can encompassinteractions between cells and between cells and extracellularcomponents, which interactions lend structural and mechanical support tobody tissues and containment of body fluids (e.g., by bloodcoagulation). However, TANGO 229 can also regulate cell-to-cell andcell-to-environment interactions which have little relevance to thestructural integrity of the animal, but which permit informationexchange between cells (e.g., cell-to-cell signaling such as that whichoccurs between helper T cells and antibody-producing B cells) or betweencells and the environment (e.g., recognition by cells of the presence ofa particular chemical entity, such as an antigen, in the environment).Certain cell-to-environment interactions mediated by TANGO 229 can alsopermit a cell which expresses it to exert an effect upon (e.g., degrade,absorb, or envelop) a component of the environment.

[0224] Involvement of TANGO 229 protein in binding of cells is anindication that TANGO 229 can be involved in disorders associated withaberrant binding or adhesion of cells with other cells, withextracellular matrix, or with foreign materials. Disorders involvingaberrant binding or adhesion of cells with other cells include bothdisorders in which cells normally bind with one another (e.g.,metastasis of normally solid tumor tissue cells away from the tumor siteof origin or immune hypersensitivity) and disorders in which the cellsdo not normally bind with one another, but do bind with one another inindividuals afflicted with the disorder (e.g., metastasis of tumor cellsinto a tissue in which the cells do not normally occur, autoimmunedisorders, infections, wherein cells with which T cells bind are notnormally present in the animal, or disorders associated with abnormalblood coagulation). Disorders involving aberrant binding or adhesion ofcells with extracellular matrix include those (e.g., metastasis ofcancerous cells through or into extracellular matrix and away from thenormal body location of the cells) in which the cells normally do, butaberrantly do not, bind with extracellular matrix as well as those(e.g., metastasis of cancers cells into extracellular matrix at bodylocations at which they do not normally occur, autoimmune disorders,liver fibrosis, abnormal blood coagulation, atherosclerosis, andarteriosclerosis) in which the cells normally do not bind withextracellular matrix, but aberrantly do. Examples of disorders involvingaberrant binding or adhesion of cells with foreign materials includethose (e.g., allergies and hypersensitivity disorders such as latexhypersensitivity) associated with aberrant binding with the foreignmaterial and disorders in which the cells normally bind with the foreignmaterial, but aberrantly do not. TANGO 229 proteins, nucleic acidsencoding them, and agents that modulate activity or expression of eitherof these can be used to prognosticate, diagnose, and treat one or moreof these disorders.

[0225] Like certain known developmental proteins (e.g., humanneuropilins; Kolodkin and Ginty (1997) Neuron 19:1159-1162), TANGO 229protein contains both a CUB domain and a factor V/VIII discoidin domain.The presence of both of these types of domains is an indication thatTANGO 229 protein is involved in mediating attraction and repulsion ofcells and translocation of cells through, past, or along other cells ortissues. For example, TANGO 229 can, alone or in conjunction with one ormore neuropilins, bind with a semaphorin protein to direct nerve growth.

[0226] Apart from regulating the rate and direction of nerve growth,TANGO 229 can regulate the rate and direction of growth of othertissues, such as vascular tissues (e.g., during angiogenesis). TANGO 229can also modulate the direction and rate of cell movement, relative toanother cell or relative to a tissue, such as movement of leukocytesthrough vascular lumenal epithelium (e.g., during leukocyticextravasation) or movement of metastatic cells through a solid tissue.Another example of such modulation is the effect that TANGO 229 can haveon the rate of cell growth, depending on contact between two cells orbetween two tissues. TANGO 229 can regulate cell growth such that thegrowth slows or substantially stops when two tissues contact one another(e.g., during wound healing). TANGO 229 is thus involved in disordersassociated with aberrant growth or movement of cells through, past, oralong other cells or tissues. Examples of disorders of these typesinclude cancerous growth and proliferation of cells, metastasis ofcancerous cells (i.e., including metastasis away from the normal bodylocation of the cells, through tissues and extracellular matrix, andinto body locations at which the cells do not normally occur),inflammation, atherosclerosis, arteriosclerosis, abnormal bloodcoagulation, asthma, and chronic obstructive pulmonary disorders. TANGO229 proteins, nucleic acids encoding them, and agents that modulateactivity or expression of either of these can be used to prognosticate,diagnose, and treat one or more of these disorders.

[0227] Like many transmembrane signaling proteins, TANGO 229 proteincomprises extracellular domains capable of interacting withenvironmental cues (e.g., the presence or absence of particular cells,proteins, or small molecules) and a cytoplasmic domain having asubstantial size. For example, several tyrosine-protein kinases (e.g.,human and murine cell adhesion kinase and neurotrophic receptor-relatedtyrosine kinase-3) comprise one or more factor V/VIII discoidin domains.The structure of TANGO 229 protein, which has several potentialphosphorylation sites, is thus an indication that the protein can beinvolved in transducing signals across the cell membrane. Binding of aligand of TANGO 229 protein with a portion of the protein located on oneside of the membrane can affect one or more characteristics (e.g.,conformation, phosphorylation state, or level or specificity ofenzymatic activity) of a portion of the protein located on the otherside. Thus, for example, a compound in the extracellular environment ofa cell which expresses TANGO 229 can bind with the extracellular domainof the protein, thereby effecting a change in a characteristic of theintracellular portion of the protein, leading to alteration of thephysiology of the cell (e.g., effected by an activity exerted by theintracellular portion of the protein on another component of the cell).The compound in the extracellular environment can, for example, be acompound dissolved or suspended in a liquid, a compound attached toanother cell of the same animal, or a compound attached to a foreigncell or virus particle. TANGO 229 protein can associate with othersignal transduction proteins in the cell membrane, thereby modulatingthe intracellular activity of those other proteins. TANGO 229 proteincan thus have a role in disorders which involve aberrant transmembranesignal transduction. Examples of signal transduction-related disordersinclude cystic fibrosis, various chronic obstructive pulmonarydisorders, inflammation, aberrant or undesirable angiogenesis, andobesity. TANGO 229 proteins, nucleic acids encoding them, and agentsthat modulate activity or expression of either of these can be used toprognosticate, diagnose, and treat one or more of these disorders.

[0228] INTERCEPT 289

[0229] A cDNA clone (designated jthLa186d06) encoding at least a portionof human INTERCEPT 289 protein was isolated from a human mixedlymphocyte reaction cDNA library. Human INTERCEPT 289 protein is atransmembrane protein which can occur in at least six alternative forms.These forms are herein designated “form 1a,” “form 1b,” “form 2a,” “form2b,” “form 3a,” and “form 3b” for convenience. The properties of andvariations among these forms are described herein.

[0230] 1a) The full length of the cDNA encoding INTERCEPT 289 proteinform 1a (FIGS. 11A-11C and SEQ ID NO: 81) is 4074 nucleotide residues.The ORF of this cDNA, nucleotide residues 179 to 742 of SEQ ID NO: 81(i.e., SEQ ID NO: 82), encodes a 188-amino acid residue protein havingthe amino acid sequence SEQ ID NO: 83.

[0231] 1b) The full length of the cDNA encoding INTERCEPT 289 proteinform 1b (FIGS. 11D-11G and SEQ ID NO: 91) is 4018 nucleotide residues.The ORF of this cDNA, nucleotide residues 179 to 712 of SEQ ID NO: 91(i.e., SEQ ID NO: 92), encodes a 178-amino acid residue protein havingthe amino acid sequence SEQ ID NO: 93.

[0232] 2a) The full length of the cDNA encoding INTERCEPT 289 proteinform 2a (FIGS. 11H-14K and SEQ ID NO: 96) is 3985 nucleotide residues.The ORF of this cDNA, nucleotide residues 162 to 656 of SEQ ID NO: 96(i.e.; SEQ ID NO: 97), encodes a 165-amino acid residue protein havingthe amino acid sequence SEQ ID NO: 98.

[0233] 2b) The full length of the cDNA encoding INTERCEPT 289 proteinform 2b (FIGS. 11L-11O and SEQ ID NO: 101) is 3958 nucleotide residues.The ORF of this cDNA, nucleotide residues 162 to 626 of SEQ ID NO: 101(i.e., SEQ ID NO: 102), encodes a 155-amino acid residue protein havingthe amino acid sequence SEQ ID NO: 103.

[0234] 3a) The full length of the cDNA encoding INTERCEPT 289 proteinform 3a (FIGS. 11P-11S and SEQ ID NO: 106) is 3925 nucleotide residues.The ORF of this cDNA, nucleotide residues 162 to 596 of SEQ ID NO: 106(i.e., SEQ ID NO: 107), encodes a 145-amino acid residue protein havingthe amino acid sequence SEQ ID NO: 108.

[0235] 3b) The full length of the cDNA encoding INTERCEPT 289 proteinform 3b (FIGS. 11T-11V and SEQ ID NO: 111) is 3898 nucleotide residues.The ORF of this cDNA, nucleotide residues 162 to 566 of SEQ ID NO: 111(i.e., SEQ ID NO: 112), encodes a 135-amino acid residue protein havingthe amino acid sequence SEQ ID NO: 113.

[0236] The mixed lymphocyte reaction library from which the cDNAsencoding INTERCEPT 289 were isolated was prepared as follows.Mononuclear cells were isolated from 50 milliliters of peripheral bloodpooled from 22 human donors. Mononuclear cells were isolated usingHISTOPAQUE™ 1077 (Sigma Chemical Co., St. Louis, Mo.) according to themanufacturer's instructions and collected in heparinized tubes. Afterpooling the mononuclear cells, CD19⁺ B cells were removed by positiveselection using MACS™ beads and a VS+ separation column (MiltenyiBiotec, Germany) according to the manufacturer's instructions.CD19⁻cells were re-suspended at an approximate density of 10×10 cellsper milliliter in RPMI medium supplemented with 10% (v/v) fetal bovineserum, antibiotics, and L-glutamine. The cells were maintained at 37° C.in a humidified incubator, and were harvested 4, 14, and 24 hoursfollowing re-suspension. Total RNA was isolated from the cells byguanidinium isothiocyanate/beta-mercaptoethanol lysis followed by cesiumchloride gradient centrifugation. Isolated RNA was treated with DNase,and the poly-A-containing fraction of total RNA was further purifiedusing OLIGOTEX™ beads (Qiagen, Inc.). About 4.4 micrograms ofpoly-A-containing RNA was used to synthesize a cDNA library using theSuperscript™ cDNA synthesis kit (Gibco BRL, Inc.; Gaithersburg, Md.).cDNA was directionally cloned into expression plasmid pMET7 vectorsusing SalI and NotI polylinker restriction endonuclease sites in orderto generate a plasmid library. Transformants were randomly selected andexpanded in culture for single-pass nucleotide sequencing.

[0237] The invention includes nucleic acid molecules which encode apolypeptide of the invention. Such nucleic acids include, for example, aDNA molecule having the nucleotide sequence listed in one of SEQ ID NOs:81, 91, 96, 101, 106, and 111, such as the portion which encodesINTERCEPT 289 protein or a domain (e.g., the extracellular domain) ofINTERCEPT 289 protein. These nucleic acids are collectively referred toas nucleic acids of the invention.

[0238] In each form, INTERCEPT 289 protein includes a transmembranedomain and a portion corresponding to an extra-membrane (presumablyextracellular) domain. In alternative embodiments, this extra-membranedomain is a cytoplasmic domain. The transmembrane domain corresponds toabout amino acid residues 7 to 27 of SEQ ID NO: 83 (i.e., SEQ ID NO: 84in form 1a), to about amino acid residues 7 to 27 of SEQ ID NO: 93(i.e., SEQ ID NO: 94 in form 1b), to about amino acid residues 7 to 27of SEQ ID NO: 98 (i.e., SEQ ID NO: 99 in form 2a), to about amino acidresidues 7 to 27 of SEQ ID NO: 103 (i.e., SEQ ID NO: 104 in form 2b), toabout amino acid residues 7 to 28 of SEQ ID NO: 108 (i.e., SEQ ID NO:109 in form 3a), and to about amino acid residues 7 to 28 of SEQ ID NO:113 (i.e., SEQ ID NO: 114 in form 3b).

[0239] Each form of INTERCEPT 289 protein also includes anotherextra-membrane portion. This portion corresponds to about amino acidresidues 28 to 188 of SEQ ID NO: 83 (i.e., SEQ ID NO: 85 in form 1a), toabout amino acid residues 28 to 178 of SEQ ID NO: 93 (i.e., SEQ ID NO:95 in form 1b), to about amino acid residues 28 to 165 of SEQ ID NO: 98(i.e., SEQ ID NO: 100 in form 2a), to about amino acid residues 28 to155 of SEQ ID NO: 103 (i.e., SEQ ID NO: 105 in form 2b), to about aminoacid residues 29 to 145 of SEQ ID NO: 108 (i.e., SEQ ID NO: 110 in form3a), and to about amino acid residues 29 to 135 of SEQ ID NO: 113 (i.e.,SEQ ID NO: 115 in form 3b).

[0240] INTERCEPT 289 proteins and nucleic acid molecules encoding themcomprise a family of molecules having certain conserved structural andfunctional features, as illustrated in FIGS. 11W and 11X-1 through11X-14.

[0241] In FIG. 11W, the amino acid sequences of various forms ofINTERCEPT 289 (“A”-“F”; SEQ ID NOs: 83, 93, 98, 103, 108, and 113) areshown, as aligned using the Wisconsin™ BestFit software (Smith andWaterman, (1981) Adv. Appl.

[0242] Math. 2:482-489; blosum62 scoring matrix; gap opening penalty10/gap extension penalty 10). In FIGS. 11X-1 through 11X-14, thenucleotide sequences (SEQ ID NOs: 81, 91, 96, 101, 106, and 11) of cDNAmolecules encoding the six forms of INTERCEPT 289 protein describedherein are aligned using the Wisconsin™ BestFit software (Smith andWaterman, (1981) Adv. Appl. Math. 2:482-489; gap opening penalty 10/gapextension penalty 10). As indicated in these figures, the various formsof INTERCEPT 289 protein differ in the length of the polypeptidesequence between the transmembrane domain and the lectin C-type domaindescribed below and in the amino acid sequence of the carboxyl-terminalportion of the protein.

[0243] INTERCEPT 289 proteins typically comprise a variety of potentialpost-translational modification sites and protein domains (oftenpositioned within a domain located at or near the protein surface), suchas those described herein in Table IVA, as predicted by computerizedsequence analysis of INTERCEPT 289 proteins using amino acid sequencecomparison software (comparing the amino acid sequence of INTERCEPT 289with the information in the PROSITE database {rel. 12.2; February 1995}and the Hidden Markov Models database {Rel. PFAM 3.3}). TABLE IV A Typeof Potential Amino Acid Residues Amino Modification Site of SEQ ID NO:## (INTERCEPT 289 form) Acid or Domain 83 (1a) 93 (1b) 98 (2a) 103 (2b)108 (3a) 113 (3b) Sequence N-glycosylation 32-35 32-35 32-35 32-35 NKSNsite 93-96 93-96 70-73 70-73 50-53 50-53 NESR 144-147 144-147 121-124121-124 101-104 101-104 NNSV 151-154 128-131 108-111 NVTN Protein kinaseC 40-42 40-42 40-42 40-42 TTR phosphorylation 63-65 63-65 TTR site178-180 155-157 135-137 SYR Casein kinase II 86-89 86-89 63-66 63-6643-46 43-46 STSE phosphorylation 91-94 91-94 68-71 68-71 48-51 48-51SWNE site 122-125 122-125  99-102  99-102 79-82 79-82 TDAE 168-171145-148 125-128 TKPE N-myristoylation 103-108 103-108 80-85 80-85 60-6560-65 GSTLAI site 150-155 127-132 107-112 GNVTNQ 165-170 142-147 122-127GLTKTF Lectin C-type  97-183  97-170  74-160  74-147  54-140  54-127 SeeFIG. domain 11

[0244] In various embodiments, the protein of the invention has at least1, 2, 4, 6, 8, 12, or more of the post-translational modification sitesand domains described in Table IVA.

[0245] An example of an additional domain present in INTERCEPT 289proteins is a lectin C-type domain. In one embodiment, the protein ofthe invention has at least one domain or signature sequence that is atleast 55%, preferably at least about 65%, 75%, 85%, or 95% identical tothis domain. C-type lectin domains are conserved among proteins (e.g.,animal lectins) which are involved in calcium-dependent binding ofcarbohydrates, although it has recently been recognized that thesedomains can also be involved in binding of proteins (Drickamer, (1988)J. Biol. Chem. 263:9557-9560; Drickamer, (1993) Prog. Nucl. Acid Res.Mol. Biol. 45:207-232; Drickamer, (1993) Curr. Opin. Struct. Biol.3:393-400). C-type lectins and their relevant properties are describedin greater in P.C.T. Publication No. WO 98/28332, which, as with allreferences cited herein, is incorporated by reference.

[0246] A cDNA clone (designated jtmMa127f05) encoding at least a portionof murine INTERCEPT 289 protein was also isolated. Murine INTERCEPT 289protein is a transmembrane protein. The properties of murine INTERCEPT289 are described below.

[0247] Murine INTERCEPT 289 protein includes a transmembrane domain anda portion corresponding to an extra-membrane domain. In one embodiment,the domain is extracellular; in an alternative embodiments, thisextra-membrane domain is a cytoplasmic domain. The transmembrane domaincorresponds to about amino acid residues 7 to 27 of SEQ ID NO: 163(i.e., SEQ ID NO: 164), and the extra-membrane portion corresponds toabout amino acid residues 28 to 190 of SEQ ID NO: 163 (i.e., SEQ ID NO:165).

[0248] Murine INTERCEPT 289 proteins typically comprise a variety ofpotential post-translational modification sites and protein domains(often positioned within a domain located at or near the proteinsurface), such as those described herein in Table IVB, as predicted bycomputerized sequence analysis of murine INTERCEPT 289 protein usingamino acid sequence comparison software (comparing the amino acidsequence of murine INTERCEPT 289 with the information in the PROSITEdatabase {rel. 12.2; February 1995} and the Hidden Markov Modelsdatabase {Rel.

[0249] PFAM 3.3}). TABLE IVB Amino Type of Potential Modification SiteAcid Residues Amino Acid or Domain of SEQ ID NO: 163 SequenceN-glycosylation site 51 to 54 NVSQ 146 to 149 NNSV 153 to 156 NVTNProtein kinase C phosphorylation site 180 to 182 SYR Casein kinase IIphosphorylation site 88 to 91 SFSE 155 to 158 TNQD N-myristoylation site105 to 110 GSTLAI 152 to 157 GNVTNQ 167 to 172 GLTKTY Lectin C-typedomain  99 to 185 See FIG. 11

[0250] In various embodiments, the protein of the invention has at least1, 2, 4, 6, 8, or more of the post-translational modification sites anddomains described in Table IVB.

[0251] INTERCEPT 289 proteins and cDNAs exhibit homology with humanmyeloid DAP12 (DNAX accessory protein, 12 kilodalton) associatedlectin-1 (MDL-1), which is described in PCT Publication No. WO 99/06557,which is also incorporated herein by reference. In FIG. 11W, the aminoacid sequences of various forms of INTERCEPT 289 (“A”-“F” and “R”; SEQID NOs: 83, 93, 98, 103, 108, 113, and 163, respectively), human MDL-1(“H”; SEQ ID NO: 86), and murine MDL-1 (“M”; SEQ ID NO: 88) proteins areshown, as aligned using the Wisconsin™ BestFit software (Smith andWaterman, (1981) Adv. Appl. Math. 2:482-489; BLOSUM62 scoring matrix;gap opening penalty 10/gap extension penalty 10). Each of the sevenforms of INTERCEPT 289 protein described herein has a lysine residue(i.e., at residue 116 of SEQ ID NOs: 83 and 93, at residue 93 of SEQ IDNOs: 98 and 103, at residue 73 of SEQ ID NOs: 108 and 113, and atresidue 118 of SEQ ID NO: 163) that is not present in the describedsequence (SEQ ID NO: 86) of human MDL-1 protein.

[0252] In the alignment shown in FIG. 11W, the amino acid sequence (SEQID NO: 83) of form 1a of INTERCEPT 289 protein is 100% identical to thatof human MDL-1 over the 187-amino acid residue overlapping region andabout 72.7% identical to that of murine MDL-1 in the 165-amino acidresidue overlapping region.

[0253] In the alignment shown in FIG. 11W, the amino acid sequence (SEQID NO: 93) of form 1b of INTERCEPT 289 protein is about 85.9% identicalto that of human MDL-1 over the 177-amino acid residue overlappingregion and about 60.0% identical to that of murine MDL-1 in the155-amino acid residue overlapping region.

[0254] In the alignment shown in FIG. 11W, the amino acid sequence (SEQID NO: 98) of form 2a of INTERCEPT 289 protein is 100% identical to thatof human MDL-1 over the 164-amino acid residue overlapping region andabout 71.5% identical to that of murine MDL-1 in the 165-amino acidresidue overlapping region.

[0255] In the alignment shown in FIG. 11W, the amino acid sequence (SEQID NO: 103) of form 2b of INTERCEPT 289 protein is about 83.8% identicalto that of human MDL-1 over the 154-amino acid residue overlappingregion and about 58.7% identical to that of murine MDL-1 in the155-amino acid residue overlapping region.

[0256] In the alignment shown in FIG. 11W, the amino acid sequence (SEQID NO: 108) of form 3a of INTERCEPT 289 protein is about 83.3% identicalto that of human MDL-1 over the 144-amino acid residue overlappingregion and about 74.5% identical to that of murine MDL-1 in the145-amino acid residue overlapping region.

[0257] In the alignment shown in FIG. 11W, the amino acid sequence (SEQID NO: 113) of form 3b of INTERCEPT 289 protein is about 63.4% identicalto that of human MDL-1 over the 134-amino acid residue overlappingregion and about 60.0% identical to that of murine MDL-1 in the135-amino acid residue overlapping region.

[0258] In the alignment shown in FIG. 1I W, the amino acid sequence (SEQID NO: 163) of murine INTERCEPT 289 protein is 100% identical to that ofmurine MDL-1 over the 190-amino acid residue overlapping region andabout 85.7% identical to that of human MDL-1 in the 188-amino acidresidue overlapping region.

[0259] In the alignment shown in FIG. 11Z-5, the nucleotide sequence(SEQ ID NO: 162) of the ORF of murine INTERCEPT 289 is about 71.8%identical to that of the ORF of human INTERCEPT 289 form 1a.

[0260] MDL-1 is a cell surface protein which is expressed by monocytesand macrophages and which binds with DAP12. DAP12 is a cell surfaceprotein which is expressed by natural killer cells, peripheral bloodgranulocytes and monocytes, macrophages, and dendritic cells. DAP12 isan immunoreceptor tyrosine-based activation motif-containing proteinwhich associates non-covalently with activating isoforms of MHC class Ireceptors on natural killer cells (Bakker et al., 1999, Proc. Natl.Acad. Sci. USA 96:9792-9796). Association of MDL-1 and DAP12 on thesurface of monocytes and macrophages and binding of associatedMDL-1/DAP12 with a ligand thereof (e.g., a surface protein,glycoprotein, or glycolipid on the surface of another cell of the sameanimal or on the surface of a foreign cell) causes activation of thosecells. Upon activation, and depending on the type of themonocyte/macrophage, the monocyte/macrophage generates an oxidativeburst, produces one or more cytokines, and other leukocyte-modulatingmolecules, releases one or more cytokines other leukocyte-modulatingmolecules, or some combination of these activities. MDL-1 and, byanalogy, INTERCEPT 289 are therefore involved in modulation of immunefunction, including modulation of antibody and cytotoxic T cellresponses, expansion of immune cell populations, inflammation, andgeneration of memory B cells.

[0261] The amino acid sequences (SEQ ID NOs: 83, 93, 98, 103, 108, and113) of the six forms of INTERCEPT 289 protein described herein werealigned with the amino acid sequence of CD94 protein (GenBank AccessionNo. 5542082) using the Wisconsin™ BestFit software (Smith and Waterman,(1981) Adv. Appl. Math. 2:482-489; BLOSUM62 scoring matrix; gap openingpenalty 10/gap extension penalty 10). The amino acid sequence identitybetween CD94 protein and INTERCEPT 289 protein was 28.0% for form 1a inthe 126-amino acid residue overlapping region, 25.2% for form 1b in the115-amino acid residue overlapping region, 28.0% for form 2a in the125-amino acid residue overlapping region, 25.2% for form 2b in the127-amino acid residue overlapping region, 27.2% for form 3a in the125-amino acid residue overlapping region, and 24.3% for form 3b in the115-amino acid residue overlapping region. CD94 protein is acell-surface protein which has a C-type lectin domain in its carboxylterminal portion and which acts as a receptor for natural killer (NK)cells. CD94 modulates the cytotoxic activity of NK cells, as well asproduction of cytokines by NK cells.

[0262] FIGS. 11Y-1 through 11Y-6 depict hydrophobicity plots of the sixforms of human INTERCEPT 289 protein described herein. Form 1acorresponds to FIGS. 11Y-1, and has the amino acid sequence SEQ ID NO:83. Form 1b corresponds to FIG. 11Y-2, and has the amino acid sequenceSEQ ID NO: 93. Form 2a corresponds to FIG. 11Y-3, and has the amino acidsequence SEQ ID NO: 98.

[0263] Form 2b corresponds to FIG. 11Y-4, and has the amino acidsequence SEQ ID NO: 103. Form 3a corresponds to FIG. 11Y-5, and has theamino acid sequence SEQ ID NO: 108. Form 3b corresponds to FIG. 11Y-6,and has the amino acid sequence SEQ ID NO: 113. Relatively hydrophobicregions are above the dashed horizontal line, and relatively hydrophilicregions are below the dashed horizontal line. As described elsewhereherein, relatively hydrophilic regions are generally located at or nearthe surface of a protein, and are more frequently effective immunogenicepitopes than are relatively hydrophobic regions. FIG. 11Z-6 depicts ahydrophobicity plot of the murine INTERCEPT 289 protein describedherein.

[0264] The predicted molecular weights of the six forms of humanINTERCEPT 289 protein described herein, without modification, is about21.5 kilodaltons for form 1a, about 20.4 kilodaltons for form 1b, about19.1 kilodaltons for form 2a, about 18.0 kilodaltons for form 2b, about16.9 kilodaltons for form 3a, and about 15.8 kilodaltons for form 3b.The predicted molecular weight of murine INTERCEPT 289, withoutmodification is about 21.7 kilodaltons.

[0265] Expression of one or more forms of INTERCEPT 289 was detected incDNA libraries prepared using human tissue and cell samples listed inTable V, wherein “+” indicates detectable expression and “+/−” indicatesweakly detectable expression. TABLE V cDNA library ExpressionPromyelocytic Leukemia Cells + Bone Marrow + D8 Dendritic Cells +/−Ovarian Ascites +/− Aortic Endothelial Cells +/− Congestive HeartFailure (left +/− ventricle)

[0266] Uses of INTERCEPT 289 Nucleic Acids,

[0267] Polypeptides, and Modulators Thereof

[0268] INTERCEPT 289 proteins are involved in disorders which affectboth tissues in which they are normally expressed and tissues in whichthey are normally not expressed. Based on the observations that cDNAcorresponding to INTERCEPT 289 occurs in a human mixed lymphocytereaction cDNA library, and that RNA corresponding to INTERCEPT 289 isdetectable by PCR amplification, using primers which specificallyamplify INTERCEPT 289 sequences, of nucleic acids (e.g., mRNA or cDNA)obtained from human leukemia, bone marrow, dendritic, ovarian ascitic,aortic endothelial, and cardiac (e.g., left ventricle cells obtainedfrom a heart afflicted with congestive heart failure) cells, it isevident that INTERCEPT 289 protein can be involved in one or morebiological processes which occur in these cells and in tissues whichcontain them. In particular, INTERCEPT 289 is involved in modulatinggrowth, proliferation, survival, differentiation, and activity of cellsof these cells and tissues (e.g., lymphocytes). Examples of disorders ofsuch cells and issues include various cancers (e.g., leukemias,lymphomas, and endothelial cancers such as ovarian cancers),atherosclerosis, arteriosclerosis, coronary artery disease, immuneinsufficiency disorders, immune hypersensitivity disorders, andcongestive heart failure disorders (e.g., myocardial infarction,cardiomegaly, and cardiac valvular defects). INTERCEPT 289 proteins,nucleic acids encoding them, and agents that modulate activity orexpression of either of these can be used to prognosticate, diagnose,and treat one or more of these disorders.

[0269] Presence of a C-type lectin domain in INTERCEPT 289 is anindication that this protein can specifically recognize particularsurfaces, such as the surface of cells of a particular type. Furthersupportive of this observation is the fact that human INTERCEPT 289proteins exhibit significant sequence identity with MDL-1 which, incooperation with DAP12 protein associated therewith, is capable ofbinding one or more ligands and activating one or more types ofmacrophages and monocytes. Aberrant activation of macrophages andmonocytes is associated with a variety of immunological disordersincluding, for example, inflammation, asthma, hypersensitivity disorders(e.g., allergies), atopic disorders (e.g., allergic rhinitis, allergicasthma, and atopic dermatitis), anaphylaxis, urticaria (i.e., hives),auto-immune disorders (e.g., rheumatoid and juvenile arthritis,rheumatism, systemic lupus erythamatosus, Grave's disease, and multiplesclerosis), graft and transplant rejection, leukemias (e.g., ALL, CML,CLL, and myelodysplastic syndrome), blood dyscrasias (e.g., multiplemyeloma), polycythemia vera, myelofibrosis, leukopenias, lymphomas(e.g., Hodgkin's disease, non-Hodgkin's lymphoma, Burkitt's lymphoma,and mycosis fungoides), bacterial, viral, and parasitic infections(e.g., sepsis, influenza, common colds, hepatitis, HIV infection,malaria, and gonorrhea), immune insufficiency (e.g., AIDS), andimmunodeficiency disorders. INTERCEPT 289 proteins, nucleic acidsencoding them, and agents that modulate activity or expression of eitherof these can be used to prognosticate, diagnose, and treat one or moreof these disorders.

[0270] INTERCEPT 309

[0271] A cDNA clone (designated jthYa038a01t1) encoding at least aportion of human INTERCEPT 309 protein was isolated from a human thyroidtissue cDNA library. Human INTERCEPT 309 protein is an integral membraneprotein having three transmembrane regions and a fourth transmembraneregion that can act as a signal sequence. Human INTERCEPT 309 protein isa claudin-like protein.

[0272] The full length of the cDNA encoding human INTERCEPT 309 protein(FIG. 12; SEQ ID NO: 121) is 1909 nucleotide residues. The ORF of thiscDNA, nucleotide residues 2 to 646 of SEQ ID NO: 121 (i.e., SEQ ID NO:122), encodes an approximately 215-amino acid residue integral membraneprotein (FIG. 12; SEQ ID NO: 123) having three transmembrane regions inits mature (181-amino acid residue; SEQ ID NO: 138) form.

[0273] The invention includes nucleic acid molecules which encode apolypeptide of the invention. Such nucleic acids include, for example, aDNA molecule having the nucleotide sequence listed in SEQ ID NO: 121,such as the portion which encodes mature INTERCEPT 309 protein, immatureINTERCEPT 309 protein, or a domain of INTERCEPT 309 protein. Thesenucleic acids are collectively referred to as nucleic acids of theinvention.

[0274] INTERCEPT 309 proteins and nucleic acid molecules encoding themcomprise a family of molecules having certain conserved structural andfunctional features.

[0275] A common domain present in INTERCEPT 309 proteins is a signalsequence. In one embodiment, a INTERCEPT 309 protein contains a signalsequence corresponding to about amino acid residues 1 to 24 of SEQ IDNO: 123 (SEQ ID NO: 124). It is recognized that the carboxyl terminalboundary of the signal sequence can be located one or two residues fromthe residue identified above (i.e., following residues 22, 23, 24, 25,or 26 of SEQ ID NO: 123). The signal sequence is cleaved duringprocessing of the mature protein.

[0276] INTERCEPT 309 proteins include three transmembrane domains andtwo pairs of extra-membrane domains that flank the cell membrane. Thethree transmembrane domains correspond to about amino acid residues 72to 92, 108 to 131, and 154 to 178 of SEQ ID NO: 123 (i.e., thetransmembrane domains having the sequences SEQ ID NOs: 126, 128, and130, respectively). One pair of extra-membrane domains corresponds toabout amino acid residues 25 to 71 and 132 to 153 of SEQ ID NO: 123(these domains having the sequences SEQ ID NOs: 125 and 129). The otherpair of extra-membrane domains corresponds to about amino acid residues93 to 107 and 179 to 215 of SEQ ID NO: 123 (these domains having thesequences SEQ ID NOs: 127 and 131). In one embodiment, the first pair ofextra-membrane domains (i.e., those having the sequences SEQ ID NOs: 125and 129) are extracellular domains and the other pair of domains arecytoplasmic domains. However, in an alternative form, the first pair ofextra-membrane domains are cytoplasmic and the other pair areextracellular domains.

[0277] It is recognized that, in certain forms, INTERCEPT 309 proteinscan have an additional number of amino acid residues at their aminoterminus. For example, the proteins can have from 1 to about 30 aminoacid residues, more commonly 1 to about 12, 1 to about 10, or 1 to about5 residues.

[0278] INTERCEPT 309 proteins typically comprise a variety of potentialpost-translational modification sites and protein domains (oftenpositioned within an extracellular or protein surface domain), such asthose described herein in Table VI, as predicted by computerizedsequence analysis of INTERCEPT 309 proteins using amino acid sequencecomparison software (comparing the amino acid sequence of INTERCEPT 309with the information in the PROSITE database {rel. 12.2; Feb, 1995} andthe Hidden Markov Models database {Rel. PFAM 3.3}). TABLE VI Amino Typeof Potential Modification Site Acid Residues Amino Acid or Domain of SEQID NO: 123 Sequence Protein kinase C phosphorylation site 184 to 186 SYR191 to 193 SHR 195 to 197 TQK 201 to 203 TGK Tyrosine kinasephosphorylation site 149 to 156 RELGEALY N-myristoylation site  7 to 12GMVGTV 39 to 44 GLWMNC 72 to 77 GLMCAA 91 to 96 GMKCTR 169 to 174 GALFCCAmidation site 201 to 204 TGKK

[0279] In various embodiments, the protein of the invention has at least1, 2, 4, 6, or all 11 of the post-translational modification sites anddomains described herein in Table VI.

[0280]FIG. 12D depicts a hydrophobicity plot of an embodiment of humanINTERCEPT 309 protein. Relatively hydrophobic regions are above thedashed horizontal line, and relatively hydrophilic regions are below thedashed horizontal line. The hydrophobic regions which corresponds toabout amino acid residues 72 to 92, 108 to 131, and 154 to 178 of SEQ IDNO: 123 are the transmembrane domains of human INTERCEPT 309 describedabove. As described elsewhere herein, relatively hydrophilic regions aregenerally located at or near the surface of a protein, and are morefrequently effective immunogenic epitopes than are relativelyhydrophobic regions. For example, the region of human INTERCEPT 309protein from about amino acid residue 90 to about amino acid residue 100appears to be located at or near the surface of the protein, while theregion from about amino acid residue 70 to about amino acid residue 85appears not to be located at or near the surface.

[0281] The predicted molecular weight of human INTERCEPT 309 proteinwithout modification and prior to cleavage of the signal sequence isabout 23.8 kilodaltons. The predicted molecular weight of the maturehuman INTERCEPT 309 protein without modification and after cleavage ofthe signal sequence is about 21.4 kilodaltons.

[0282] INTERCEPT 309 protein exhibits amino acid sequence homology withmurine claudin-8 protein, as indicated in the alignment (made using theALIGN software {Myers and Miller (1989) CABIOS, ver. 2.0}; pam120.matscoring matrix; gap opening penalty=12, gap extension penalty=4) of theamino acid sequences of INTERCEPT 309 (SEQ ID NO: 123) and murineclaudin-8 (SEQ ID NO: 132) proteins shown in FIG. 12S. In thisalignment, the two amino acid sequences are about 80.0% identical.Furthermore, INTERCEPT 309 cDNA (SEQ ID NO: 121) is about 83.1%identical to the nucleotide sequence of cDNA encoding murine claudin-8(SEQ ID NO: 133; GenBank accession no. AF087826) over the 639-residueoverlapping region, as indicated in the alignment (made using the ALIGNsoftware; pam120.mat scoring matrix; gap opening penalty=12, gapextension penalty=4) shown in FIGS. 12L through 12R.

[0283] An alignment (made using the ALIGN software; pam120.mat scoringmatrix; gap opening penalty=12, gap extension penalty=4) of thenucleotide sequences of a cDNA clone (SEQ ID NO: 134; GenBank accessionno. AL049977) obtained from human fetal brain tissue and INTERCEPT 309cDNA (SEQ ID NO: 121) is shown in FIGS. 12E through 12K and indicates100% sequence identity between the sequences in the overlapping portion.The overlapping portion does not overlap the INTERCEPT 309 ORF, with theexception of nucleotide residues 1 and 28-32. It is recognized that‘overlap’ of the human fetal brain cDNA clone sequence with these ORFresidues is an artifact of the ALIGN software, and does not representmeaningful homology between residues 1 and 28-32 of the INTERCEPT 309ORF and the corresponding residues of the human fetal brain cDNA clone.Nonetheless, isolation of this cDNA clone from fetal brain tissue is anindication that INTERCEPT 309 protein is expressed in fetal braintissue.

[0284] An alignment (made using the LALIGN software {Huang and Miller,1991, Adv. Appl. Math. 12:373-381}; pam120 scoring matrix, gap openingpenalty=12, gap extension penalty=4) of the nucleotide sequence ofINTERCEPT 309 cDNA (SEQ ID NO: 121) with the nucleotide sequenceencoding murine latent transforming growth factor-beta binding protein-3(LTBP-3) indicated that the two sequences were 40.3% identical in a1969-nucleotide residue overlapping portion.

[0285] As disclosed in P.C.T. Publication No. WO 95/22611, latenttransforming growth factor-beta binding protein 3 (LTBP-3) is a secretedprotein that is expressed in murine epithelial, parenchymal, and stromalduring embryonic development. LTBP-3 is thought to exhibit one or moreof four activities i) modulating intracellular-biosynthesis of latenttransforming growth factor-beta;

[0286] ii) binding latent transforming growth factor-beta withextracellular matrix;

[0287] iii) modulating activation of latent transforming growthfactor-beta complexes; and

[0288] iv) targeting latent transforming growth factor-beta complexes tothe cell surface.

[0289] An alignment (made using the ALIGN software; pam120.mat scoringmatrix, gap opening penalty=12, gap extension penalty=4) of the aminoacid sequence of INTERCEPT 309 cDNA (SEQ ID NO: 123) with the amino acidsequence of human peripheral myelin protein (PMP-22) indicated that thetwo protein sequences are 17.2% identical. PMP-22 is involved inmyelination of peripheral nerves, particularly during development.

[0290] Individual alignments (made using the Wisconsin™ BestFitsoftware; Smith and Waterman (1981) Adv. Appl. Math. 2:482-489; blosum62scoring matrix, gap opening penalty 10/gap extension penalty 10) of theamino acid sequence (SEQ ID NO: 123) of INTERCEPT 309 with the aminoacid sequences of human (SEQ ID NO: 135; GenBank Accession No. 4502877)and murine (SEQ ID NO: 136; GenBank Accession No. BAA22985) receptors ofClostridium perfringens enterotoxin (CPE) and with the amino acidsequence (SEQ ID NO: 137) encoded by rat ventral prostate tissue duringandrogen withdrawal-induced tissue regression were manually aligned (byinserting a ‘blank’ at position 1 of the rRPV nucleotide sequence). Themanually aligned alignments are shown in FIG. 12T. The amino acidsequence of INTERCEPT 309 protein is about 43% identical to the humanCPE receptor amino acid sequence, about 45% identical to the murine CPEreceptor amino acid sequence, and about 43% identical to the amino acidsequence encoded by the transcript obtained from regressing rat ventralprostate tissue.

[0291] Expressed sequence tags (ESTs) which exhibit at least limitednucleotide sequence identity with SEQ ID NO: 121 have been isolated fromhuman and murine liver, kidney, prostate, and colon tissues.

[0292] Uses of INTERCEPT 309 Nucleic Acids,

[0293] Polypeptides, and Modulators Thereof

[0294] INTERCEPT 309 proteins are involved in disorders which affectboth tissues in which they are normally expressed and tissues in whichthey are normally not expressed. Based on the observations that cDNAcorresponding to INTERCEPT 309 occurs in human thyroid and fetal braincDNA libraries, and that ESTs have been isolated from liver, kidney,prostate, and colon tissues, it is evident that INTERCEPT 309 protein isinvolved in one or more biological processes which occur in thesetissues. In particular, INTERCEPT 309 is involved in modulating growth,proliferation, survival, differentiation, and activity (e.g., thyroidsecretion activity) of cells of these tissues. Thus, INTERCEPT 309 has arole in disorders which affect the brain, thyroid, and other tissues andone or more of growth, proliferation, survival, differentiation,activity, morphology, and movement/migration of cells in those tissues,as well as the biological function of organs (e.g., the brain, liver,colon, prostate, kidneys, and thyroid) comprising such tissues. Relevantdisorders which involve these tissues are discussed separately below.

[0295] As indicated by its similarity to murine claudin-8 (e.g., asshown in FIG. 12S), INTERCEPT 309 is a claudin-like protein, and canexhibit one or more of the activities exhibited by murine claudin-8 andother claudins. Claudins are proteins that are involved in formation,maintenance, and regulation of tight junctions, which are intercellularjunctions that occur between cells of tissues (e.g., epithelia andendothelia) having selective permeability (Morita et al. (1999) Proc.Natl. Acad. Sci.

[0296] USA 96:511-516). Tight junctions can be associated with actinfibrils, and claudins can mediate interactions between actin fibrils andother components of the tight junction. Tissues in which tight junctionsoccur between adjacent cells can form sheets or other structures whichexhibit selective trans-tissue permeability and in which the membraneand membrane-bound components of tissue-spanning cells can beselectively localized to one side (e.g., apical or basolateral side) ofthe tissue. By way of example, epithelial and endothelial tissues ofkidney, liver, lung, and thyroid form barriers which permittransepithelial/transendothelial passage of certain compounds and cells(e.g., secreted/excreted products and immune system cells), but notothers. Tight junction alterations have also been associated with tumordifferentiation, particularly in thyroid tumors (Kerjaschki et al.(1979) Am. J. Pathol. 96:207-225; Cochand-Priollet et al. (1998)Ultrastruct. Pathol. 22:413-420). INTERCEPT 309 can have a role in eachof these functions, both in normal tissue and in aberrant tissue (e.g.,tissue of a patient afflicted with a disorder that affects the tissue).

[0297] An important feature of tight junctions is that the permeabilityof a tissue comprising such intercellular junctions can be regulated bycellular and other (e.g., endocrine) processes. Thus, depending on thecellular or other influences exerted on the components of the tightjunction, the permeability of the tissue to water, solutes (e.g., urea),proteins (e.g., hormones), and immune cells (e.g., T cells andmacrophages) can be regulated (Stevenson (1999) J. Clin. Invest.104:3-4). Regulation of transmembrane permeability is critical to thefunction of many organs (e.g., kidney, colon, thyroid, liver, prostate,etc.). INTERCEPT 309, being a claudin-like protein can regulatetransmembrane permeability in organs and tissues in which it is normallyor aberrantly expressed.

[0298] One or more transmembrane proteins associated with tightjunctions mediate transmembrane signal transduction which regulates,inter alia, the permeability of the junction (Fanning et al., (1999) J.Am. Soc. Nephrol. 10:1337-1345). For example, inhibition of proteintyrosine phosphorylation (a common activity associated withtransmembrane signaling) has been associated with aberrant thyroidepithelial cell junction formation (Yap et al., (1997) Endocrinology138:2315-2324). INTERCEPT 309, being a transmembrane protein associatedwith tight junctions and having a potential tyrosine kinasephosphorylation site at residues 149-156 of SEQ ID NO: 123, can beinvolved in transmembrane transduction of signals between the cellinterior and the extracellular milieu, including signal transductionassociated with regulation of tight junction function.

[0299] Claudins can also participate in cell-to-cell adhesive processesthat do not necessarily involve tight junction formation. Examples ofsuch mechanisms include binding between cells forming the blood-brainbarrier, adhesion of myelin to nerve fibers and to itself, and bindingbetween skin cells to form a barrier to the passage of moisture andsolutes to and from the environment. Similarity between the amino acidsequences of INTERCEPT 309 and PMP-22 is also indicative of a role ofINTERCEPT 309 protein in mediating adhesion between myelin-producingcells and nerve cells (e.g., between Schwann cells and peripheral nervecells). INTERCEPT 309 can therefore have a role in disorders (e.g.,multiple sclerosis) involving aberrant (including insufficient)myelination or demyelination of nerve cells.

[0300] INTERCEPT 309, being a cell surface claudin-like protein, can bea substrate for interaction of pathogens (e.g., bacteria, toxins, andviruses) with host cells, and can mediate interaction of pathogens withcells which express INTERCEPT 309.

[0301] For example, Morita et al. (supra) determined that a murineclaudin is a receptor for Clostridium perfringens enterotoxin (CPE).Similarity between the amino acid sequences of murine claudin-8 andINTERCEPT 309 indicates that INTERCEPT 309 can act as a receptor forCPE. Furthermore, amino acid sequence similarity between INTERCEPT 309and other human and murine CPE receptors (e.g., GenBank Accession Nos.4502877 and BAA22985, as indicated in FIG. 12T) is a further indicationthat INTERCEPT 309 can mediate interaction of CPE with cells upon whichCPE acts. INTERCEPT 309 proteins, nucleic acids encoding them, andagents that modulate activity or expression of either of these can beused to prognosticate, diagnose, and treat disorders mediated by C.perfringens. Such disorders include, by way of example, gastrointestinaldisorders (e.g., diarrhea, gastroenteritis, and other disordersassociated with food poisoning, and certain types of pseudomembranouscolitis), disorders associated with wound healing (e.g., gangrene), andother pathogenic infections (e.g., sepsis with or without intravascularhemolysis). INTERCEPT 309 can, of course, also mediate interaction ofother pathogens with cells which express it.

[0302] Being a claudin-like protein, INTERCEPT 309 can be involved information, maintenance, and regulation of structures (e.g.,transmembrane protein complexes including INTERCEPT 309) that regulatethe permeability of cell membranes with regard to various molecules andmacromolecules. Regulation of trans-tissue (i.e., intercellular)diffusion of extracellular components (e.g., water, solutes, and immunecells) and diffusion of membrane-bound and integral membrane componentsfrom one side of a tissue (e.g., the apical face of an epithelium) tothe other (e.g., the basolateral face of the same epithelium; i.e.,paracellular diffusion) can be modulated by INTERCEPT 309 proteins andnucleic acids and by small molecules which interact with INTERCEPT 309proteins and nucleic acids encoding them. Actin is known to beassociated with tight junction components, and modifications to theactin cytoskeleton of a cell can modulate tight junction-regulatedintercellular and paracellular diffusion. Thus, compositions whichaffect the interaction between actin and INTERCEPT 309 protein canmodulate tight junction regulation of intercellular and paracellulardiffusion. In addition, agents which act directly on an INTERCEPT 309protein or nucleic acid, without affecting the interaction between theclaudin and actin, can be used to modulate tight junction regulation ofintercellular and paracellular diffusion. INTERCEPT 309 protein can alsoact as a receptor for C. perfringens enterotoxin and for otherpathogens, and INTERCEPT 309 proteins, as described herein, can be usedto modulate C. perfringens enterotoxin binding and toxicity, as well asbinding of other pathogens with cells and tissues which expressINTERCEPT 309.

[0303] The fact that cDNA encoding INTERCEPT 309 was isolated from humanthyroid and fetal brain cDNA libraries and the fact that INTERCEPT 309have been isolated from liver, kidney, prostate, and colon tissuesindicates that INTERCEPT 309 can have a role in disorders of thesetissues, particularly including those characterized above. Examples ofdisorders in which INTERCEPT 309 can have a role are described in thefollowing paragraphs a)-f), which are organized, for convenience, bytissue type.

[0304] a) Examples of brain disorders in which INTERCEPT 309 can haverole include both CNS disorders, CNS-related disorders, focal braindisorders, global-diffuse cerebral disorders, and other neurological andcerebrovascular disorders. CNS disorders include, but are not limited tocognitive and neurodegenerative disorders such as Alzheimer's disease,senile dementia, Huntington's disease, amyotrophic lateral sclerosis,and Parkinson's disease, as well as Gilles de 1a Tourette's syndrome,autonomic function disorders such as hypertension and sleep disorders(e.g., insomnia, hypersomnia, parasomnia, and sleep apnea),neuropsychiatric disorders (e.g., schizophrenia, schizoaffectivedisorder, attention deficit disorder, dysthymic disorder, majordepressive disorder, mania, and obsessive-compulsive disorder),psychoactive substance use disorders, anxiety, panic disorder, andbipolar affective disorder (e.g., severe bipolar affective disorder andbipolar affective disorder with hypomania and major depression).CNS-related disorders include disorders associated with developmental,cognitive, and autonomic neural and neurological processes, such aspain, appetite, long term memory, and short term memory. Examples offocal brain disorders include aphasia, apraxia, agnosia, and amnesias(e.g., posttraumatic amnesia, transient global amnesia, and psychogenicamnesia). Global-diffuse cerebral disorders with which INTERCEPT 309 isassociated include coma, stupor, obtundation, and disorders of thereticular formation. Cerebrovascular disorders include ischemicsyndromes (e.g., stroke), hypertensive encephalopathy, hemorrhagicdisorders, and disorders involving aberrant function of the blood-brainbarrier (e.g., CNS infections such as meningitis and encephalitis,aseptic meningitis, metastasis of non-CNS tumor cells into the CNS,various pain disorders such as migraine, and CNS-related adverse drugreactions such as head pain, sleepiness, and confusion). INTERCEPT 309proteins, nucleic acids encoding them, and agents that modulate activityor expression of either of these can be used to prognosticate, diagnose,and treat one or more of these disorders.

[0305] b) Examples of thyroid disorders with which INTERCEPT 309proteins and nucleic acids encoding them can be involved include hyper-and hypothyroidism, goiter, thyroiditis, thyroid cancers (e.g., adenomasand carcinomas), and autoimmune diseases involving thyroid autoantigenssuch as thyroglobulin and thyroperoxidase. INTERCEPT 309 proteins,nucleic acids encoding them, and agents that modulate activity orexpression of either of these can be used to prognosticate, diagnose,and treat one or more of these disorders.

[0306] c) Kidney disorders with which INTERCEPT 309 proteins and nucleicacids encoding them can be involved include acute and chronic renalfailure, immunologically-mediated renal disorders (i.e., involving bothrenal antigens and extra-renal antigens that have become located withinthe kidneys), glomerular diseases such as acute and progressivenephritic syndromes and nephrotic syndromes, acute and chronictubulointerstitial nephritis, infections of the kidney, nephrotoxicdisorders (i.e., including those associated with antibiotics,analgesics, anti-cancer agents, anti-epileptic agents, etc.),nephrogenic diabetes insipidus, hereditary chronic nephropathies,urinary incontinence, urinary calculus formation, kidney infections, andkidney neoplasms. INTERCEPT 309 proteins, nucleic acids encoding them,and agents that modulate activity or expression of either of these canbe used to prognosticate, diagnose, and treat one or more of thesedisorders.

[0307] d) Examples of liver disorders in which INTERCEPT 309 can have arole include the liver disorders described elsewhere in this disclosure.

[0308] e) Prostate disorders with which INTERCEPT 309 proteins andnucleic acids encoding them can be involved include the prostatedisorders described elsewhere in this disclosure.

[0309] f) Disorders of the colon in which INTERCEPT 309 can have a roleinclude, for example, diarrhea, constipation, gastroenteritis,malabsorption syndromes such as celiac disease and tropical sprue,inflammatory bowel diseases such as Crohn's disease and ulcerativecolitis, antibiotic-associated colitis, functional bowel disorders suchas irritable bowel syndrome and functional diarrhea, congenitalanomalies (e.g., megacolon and imperforate anus), idiopathic disorders(e.g., diverticular disease such as diverticulosis and diverticulitisand melanosis coli), vascular lesions (e.g., ischemic colitis,hemorrhoids, angiodysplasia), inflammatory diseases (e.g., idiopathiculcerative colitis, pseudomembranous colitis, and lymphopathiavenereum), and colon tumors (e.g., hyperplastic polyps, adenomatouspolyps, bronchogenic cancer, colonic carcinoma, squamous cell carcinoma,adenoacanthomas, sarcomas, lymphomas, argentaffinomas, carcinoids, andmelanocarcinomas). INTERCEPT 309 proteins, nucleic acids encoding them,and agents that modulate activity or expression of either of these canbe used to prognosticate, diagnose, and treat one or more of thesedisorders.

[0310] INTERCEPT 309 (like claudins) regulates intercellularpermeability in tissues through which one may wish to modulate thepassage of drugs or other agents. Such tissues include, for example, theblood-brain barrier (e.g., at the choroid plexus), vascular endothelium,and liver epithelial tissues (i.e., other than fenestrated hepaticvascular epithelia). By way of example, one may wish either to enhancethe permeability of a tissue with respect to a drug (e.g., a drug forwhich enhanced blood-brain barrier permeability is desired) or to reducethe permeability of a tissue with respect to a drug (e.g., a drug forwhich reduction of hepatic sequestration is desired). INTERCEPT 309proteins and nucleic acids, and other compounds which modulate thestructure or activity of INTERCEPT 309 proteins and nucleic acids, canbe used to regulate the permeability of such tissues.

[0311] In addition to its structural and functional similarity withclaudin proteins, INTERCEPT 309 protein is also similar in sequence toat least one protein regulator of apoptosis. As shown in FIG. 12T, theamino acid sequence of INTERCEPT 309 is similar to the amino acidsequence of a protein (rRPV) which is expressed specifically inregressing rat ventral prostate tissue and epididymis. As described byBriehl et al. (1991, Mol. Endocrinol. 5:1381-1388), expression of thisrat protein is elevated 3- to 8-fold in ventral prostate tissue uponinduction of tissue regression mediated by withdrawal of androgens.Androgen withdrawal induces apoptosis in rat ventral prostate tissue.Thus, the rat protein described by Briehl et al. (supra) is anapoptosis-associated protein. INTERCEPT 309, having a sequence similarto that of rRPV, can also modulate apoptosis in tissues in which it isexpressed.

[0312] Apoptosis is a process of controlled cell death that occursnormally in many tissues in which cell division occurs essentiallycontinuously. Examples of such tissues include nearly all tissues otherthan adult brain and cardiac muscle tissues, and particularly includerapidly-growing and rapidly-replaced tissues such as epithelial andendothelial tissues. Elimination of abnormal or damaged cells from atissue (other than adult brain or cardiac muscle tissues) frequentlyoccurs by apoptosis of the abnormal or damaged cells, rather than bynecrosis, which can lead to inflammation. Apoptosis thus represents animportant homeostatic process in healthy individuals, and aberrance innormal apoptosis can lead to occurrence of one or more disorders.INTERCEPT 309 (which, as described above is similar to the rat proteinof Briehl et al.) can also be associated with apoptosis. INTERCEPT 309can modulate apoptosis in tissues in which it is expressed, both undernormal (i.e., homeostatic, non-disorder-associated) conditions and intissue affected by a disorder associated with aberrant apoptosis.Disorders associated with aberrant apoptosis include both disorders inwhich apoptosis occurs to a supra-normal degree (e.g., humanimmunodeficiency virus-mediated depletion of CD4⁺ T cells) and disordersin which apoptosis is inhibited, relative to normal levels (e.g.,various cancers and viral infections characterized by survival ofvirus-infected cells). Examples of disorders associated with aberrantapoptosis include substantially all cancers and viral infections,obesity, diabetes, atherosclerosis, arteriosclerosis, coronary arterydisease, and angiogenesis. INTERCEPT 309 proteins, nucleic acidsencoding them, and agents that modulate activity or expression of eitherof these can be used to prognosticate, diagnose, and treat one or moreof these disorders.

[0313] MANGO 419

[0314] A cDNA clone (designated cohqf013f05) encoding at least a portionof human MANGO 419 protein was isolated from a human cDNA libraryprepared from prostate carcinoma tissue which had metastasized to liver.Human MANGO 419 protein is a secreted protein.

[0315] The full length of the cDNA encoding human MANGO 419 protein(FIG. 13; SEQ ID NO: 141) is 323 nucleotide residues. The ORF of thiscDNA, nucleotide residues 84 to 323 of SEQ ID NO: 141 (i.e., SEQ ID NO:142), encodes an 80-amino acid residue (or longer) protein (FIG. 13; SEQID NO: 143), corresponding to a 56-residue (or longer) secreted matureprotein.

[0316] The invention thus includes purified human MANGO 419 protein,both in the form of the immature 80 amino acid residue protein (SEQ IDNO: 143) and in the form of the mature 56 amino acid residue protein(SEQ ID NO: 145). Mature human MANGO 419 proteins can be synthesizedwithout the signal sequence polypeptide at the amino terminus thereof,or they can be synthesized by generating immature MANGO 419 protein andcleaving the signal sequence therefrom.

[0317] MANGO 419 protein can have one or more amino acid residuesattached at the carboxyl terminal end thereof. By way of example, therecan be from 1 to about 500, 1 to 100, 1 to 50, 1 to 30, 1 to 20, or 1 to10 additional amino acid residues.

[0318] The invention includes nucleic acid molecules which encode apolypeptide of the invention. Such nucleic acids include, for example, aDNA molecule having the nucleotide sequence listed in SEQ ID NO: 141,such as the portion which encodes mature MANGO 419 protein, immatureMANGO 419 protein, or a domain of MANGO 419 protein. These nucleic acidsare collectively referred to as nucleic acids of the invention.

[0319] MANGO 419 proteins and nucleic acid molecules encoding themcomprise a family of molecules having certain conserved structural andfunctional features.

[0320] A common domain present in MANGO 419 proteins is a signalsequence. In one embodiment, a MANGO 419 protein contains a signalsequence corresponding to the portion of the protein from amino acidresidue 1 to about amino acid residue 24 of SEQ ID NO: 143 (SEQ ID NO:144). It is recognized that the carboxyl terminal boundary of the signalsequence can be located one or two residues from the residue identifiedabove (i.e., following residues 22, 23, 24, 25, or 26 of SEQ ID NO:143). The signal sequence is cleaved during processing of the matureprotein.

[0321] MANGO 419 proteins typically comprise a variety of potentialpost-translational modification sites and protein domains (oftenpositioned within an extracellular or protein surface domain), such asthose described herein in Table VII, as predicted by computerizedsequence analysis of MANGO 419 proteins using amino acid sequencecomparison software (comparing the amino acid sequence of MANGO 419 withthe information in the PROSITE database {rel. 12.2; February 1995} andthe Hidden Markov Models database {Rel. PFAM 3.3}). TABLE VII Amino Typeof Potential Modification Site Acid Residues Amino Acid or Domain of SEQID NO: 143 Sequence Casein kinase II phosphorylation site 31 to 34 TFGE55 to 58 SSDD N-myristoylation site 43 to 48 GCRRCC

[0322] In various embodiments, the protein of the invention has at least1, 2, or all 3 of the post-translational modification sites and domainsdescribed herein in Table VII.

[0323] The signal peptide prediction program SIGNALP (Nielsen et al.(1997) Protein Engineering 10:1-6) predicted that human MANGO 419protein includes an approximately 24 amino acid residue signal peptide(amino acid residues 1 to about 24 of SEQ ID NO: 143; SEQ ID NO: 144)preceding the mature MANGO 419 protein (amino acid residues 25 to 80 ofSEQ ID NO: 143; SEQ ID NO: 145).

[0324]FIG. 13B depicts a hydrophobicity plot of human MANGO 419 protein.Relatively hydrophobic regions are above the dashed horizontal line, andrelatively hydrophilic regions are below the dashed horizontal line. Thehydrophobic region which corresponds to amino acid residues 1 to about24 of SEQ ID NO: 143 is the signal sequence of human MANGO 419 (SEQ IDNO: 144). As described elsewhere herein, relatively hydrophilic regionsare generally located at or near the surface of a protein, and are morefrequently effective immunogenic epitopes than are relativelyhydrophobic regions. For example, the region of human MANGO 419 proteinfrom about amino acid residue 35 to about amino acid residue 55 appearsto be located at or near the surface of the protein, while the regionfrom about amino acid residue 60 to about amino acid residue 65 appearsnot to be located at or near the surface.

[0325] The predicted molecular weight of human MANGO 419 protein withoutmodification and prior to cleavage of the signal sequence is about 8.8kilodaltons. The predicted molecular weight of the mature human MANGO419 protein without modification and after cleavage of the signalsequence is about 6.2 kilodaltons.

[0326] Expressed sequence tags (ESTs) which exhibit homology with SEQ IDNO: 141 have been isolated from murine mammary and embryonic tissues.Those ESTs have sequences that are similar to the sequence of a nucleicacid encoding an inner ear-specific collagen precursor.

[0327] Uses of MANGO 419 Nucleic Acids,

[0328] Polypeptides, and Modulators Thereof

[0329] MANGO 419 proteins are involved in disorders which affect bothtissues in which they are normally expressed and tissues in which theyare normally not expressed. Based on the observations that cDNAcorresponding to MANGO 419 occurs in a human metastatic prostatecarcinoma cDNA library, and that ESTs obtained from mammary andembryonic tissues exhibit homology with MANGO 419 cDNA, it is evidentthat MANGO 419 protein can be involved in one or more biologicalprocesses which occur in these tissues. In particular, MANGO 419 can beinvolved in modulating growth, proliferation, survival, differentiation,and activity of cells of these tissues (e.g., mammary, prostate, andother epithelial and endothelial cells). MANGO 419 can have a role indisorders which affect epithelial and endothelial tissues including, forexample, prostate, breast, and embryonic tissues. MANGO 419 proteins,nucleic acids encoding them, and small molecules which interact witheither of these can be used to prognosticate, diagnose, and treatdisorders of epithelial and endothelial tissues, particularly includingcarcinogenesis and metastasis of epithelial and endothelial neoplasms,such as prostate and mammary cancers.

[0330] Recovery of a cDNA encoding MANGO 419 from a library preparedusing metastatic prostate carcinoma cells also indicates that MANGO 419can affect the ability and propensity of a cell to adhere with othercells or with extracellular surfaces, and that MANGO 419 can affect theability of cells which express it to move through other tissues andthrough extracellular matrix. Furthermore, the fact that MANGO 419 is asecreted protein indicates that it can be used (e.g., by detecting it ina body fluid) as a marker for the metastatic state of cancers,particularly including epithelial carcinomas.

[0331] Expression of MANGO 419 protein in epithelial tissues such asprostate and mammary tissues is an indication that MANGO 419 protein andnucleic acids which encode them can be involved in disorders ofepithelial and endothelial tissues. Examples of disorders of epithelialand endothelial tissues include cell binding, adhesion, andproliferation disorders and epithelial/endothelial permeability-relateddisorders. MANGO 419 protein is involved in disorders associated withaberrant binding or adhesion of cells with other cells, withextracellular matrix, or with foreign materials. Disorders involvingaberrant binding or adhesion of cells with other cells include bothdisorders in which cells normally bind with one another (e.g.,metastasis of a cancerous cells away from a solid tissue site at whichthey normally occur or immune hypersensitivity) and disorders in whichthe cells do not normally bind with one another, but do bind with oneanother in individuals afflicted with the disorder (e.g., autoimmunedisorders, infections, wherein cells with which T cells bind are notnormally present in the animal, or disorders associated with abnormalblood coagulation). Disorders involving aberrant binding or adhesion ofcells with extracellular matrix include those (e.g., metastasis of anormally solid tumor tissue away from it site of origin) in which thecells normally do, but aberrantly do not, bind with extracellular matrixas well as those (e.g., metastasis of tumor cells into a tissue in whichthe cells do not normally occur, autoimmune disorders, liver fibrosis,abnormal blood coagulation, atherosclerosis, and arteriosclerosis) inwhich the cells normally do not bind with extracellular matrix, butaberrantly do. Examples of disorders involving aberrant binding oradhesion of cells with foreign materials include those (e.g., allergiesand hypersensitivity disorders such as latex hypersensitivity)associated with aberrant binding with the foreign material and disordersin which the cells normally bind with the foreign material, butaberrantly do not. MANGO 419 proteins, nucleic acids encoding them, andagents that modulate activity or expression of either of these can beused to prognosticate, diagnose, and treat one or more of thesedisorders.

[0332] Expression of MANGO 419 protein in epithelial tissues such asprostate and mammary tissues is an indication that MANGO 419 proteinsand nucleic acids can be involved in disorders associated with aberrantpermeability of epithelial tissues (i.e., aberrant permeability withregard to water, solutes, proteins, immune cells, and pathogens). Suchdisorders include, by way of example, kidney disorders, liver disorders,gastrointestinal disorders, endocrine and exocrine disorders, prostatedisorders, gynecological disorders, skin disorders, and brain disorders.Examples of disorders of these types are described separately, forconvenience, in the following paragraphs a)-h).

[0333] a) Kidney disorders with which MANGO 419 proteins and nucleicacids encoding them can be involved include the kidney disordersdescribed elsewhere in this disclosure. MANGO 419 proteins, nucleicacids encoding them, and agents that modulate activity or expression ofeither of these can be used to prognosticate, diagnose, and treat one ormore of these disorders.

[0334] b) Examples of liver disorders in which MANGO 419 can have a roleinclude the liver disorders described elsewhere in this disclosure.MANGO 419 proteins, nucleic acids encoding them, and agents thatmodulate activity or expression of either of these can be used toprognosticate, diagnose, and treat one or more of these disorders.

[0335] c) Disorders of the gastrointestinal tract in which MANGO 419 canhave a role include, for example, gastroesophageal reflux disease,gastric ulcers, gastritis, appendicitis, peritonitis, diarrhea,constipation, gastroenteritis, malabsorption syndromes such as celiacdisease and tropical sprue, inflammatory bowel diseases such as Crohn'sdisease and ulcerative colitis, antibiotic-associated colitis,functional bowel disorders such as irritable bowel syndrome andfunctional diarrhea, diverticular diseases such as diverticulosis anddiverticulitis, and benign and malignant neoplasms of the colon. MANGO419 proteins, nucleic acids encoding them, and agents that modulateactivity or expression of either of these can be used to prognosticate,diagnose, and treat one or more of these disorders.

[0336] d) Examples of endocrine and exocrine disorders with which MANGO419 proteins and nucleic acids encoding them can be involved includediabetes mellitus, hypoglycemia, glucagon disorders, pituitary disorderssuch as diabetes insipidus, thyroid disorders such as hyper- andhypothyroidism, adrenal disorders such as Cushing's syndrome andhyperaldosteronism, multiple endocrine neoplasias, polyglandulardeficiency syndromes, epithelial breast cancers, biliary calculi,cholecystitis, and neoplasms of the bile ducts, chronic and acute renalfailure, immunologically mediated renal diseases, glomerular diseasessuch as acute neprhitic syndrome and nephrotic syndrome,tubulointerstitial diseases, nephrotoxic disorders, and infections ofthe kidney, goiter, thyroiditis, thyroid cancers, and autoimmunediseases involving endocrine (e.g., thyroid) autoantigens. MANGO 419proteins, nucleic acids encoding them, and agents that modulate activityor expression of either of these can be used to prognosticate, diagnose,and treat one or more of these disorders.

[0337] e) Prostate disorders with which MANGO 419 proteins and nucleicacids encoding them can be involved include prostate neoplasms, benignprostatic hyperplasia, and benign prostatic hypertrophy. MANGO 419proteins, nucleic acids encoding them, and agents that modulate activityor expression of either of these can be used to prognosticate, diagnose,and treat one or more of these disorders.

[0338] f) Gynecological disorders in which MANGO 419 can have a roleinclude ovarian, cervical, vulvar, and vaginal cancers, infertility, andendometriosis. MANGO 419 proteins, nucleic acids encoding them, andagents that modulate activity or expression of either of these can beused to prognosticate, diagnose, and treat one or more of thesedisorders.

[0339] g) Skin disorders with which MANGO 419 can be associated includepsoriasis, infections, wounds (and healing of wounds), inflammation,dermatitis, acne, and benign and malignant dermatological tumors.MANGO-419 proteins, nucleic acids encoding them, and agents thatmodulate activity or expression of either of these can be used toprognosticate, diagnose, and treat one or more of these disorders.

[0340] h) Examples of brain disorders in which MANGO 419 can have a roleinclude the brain disorders described elsewhere in this disclosure.MANGO 419 proteins, nucleic acids encoding them, and agents thatmodulate activity or expression of either of these can be used toprognosticate, diagnose, and treat one or more of these disorders.

[0341] INTERCEPT 429

[0342] A cDNA clone (designated jchrd012h06) encoding at least a portionof human INTERCEPT 429 protein was isolated from a human heart cDNAlibrary.

[0343] Human INTERCEPT 429 protein is a transmembrane protein.

[0344] The full length of the cDNA encoding human INTERCEPT 429 protein(FIG. 14; SEQ ID NO: 151) is 546 nucleotide residues. The ORF of thiscDNA, nucleotide residues 95 to 439 of SEQ ID NO: 151 (i.e., SEQ ID NO:152), encodes a 115-amino acid residue protein (FIG. 14; SEQ ID NO:153), corresponding to a 93-residue transmembrane mature protein.

[0345] The invention includes purified human INTERCEPT 429 protein, bothin the form of the immature 115 amino acid residue protein (SEQ ID NO:153) and in the form of the mature 93 amino acid residue protein (SEQ IDNO: 155). Mature human INTERCEPT 429 proteins can be synthesized withoutthe signal sequence polypeptide at the amino terminus thereof, or theycan be synthesized by generating immature INTERCEPT 429 protein andcleaving the signal sequence therefrom.

[0346] The invention includes nucleic acid molecules which encode apolypeptide of the invention. Such nucleic acids include, for example, aDNA molecule having the nucleotide sequence listed in SEQ ID NO: 151,such as the portion which encodes mature INTERCEPT 429 protein, immatureINTERCEPT 429 protein, or a domain of INTERCEPT 429 protein. Thesenucleic acids are collectively referred to as nucleic acids of theinvention.

[0347] INTERCEPT 429 proteins and nucleic acid molecules encoding themcomprise a family of molecules having certain conserved structural andfunctional features.

[0348] A common domain present in INTERCEPT 429 proteins is a signalsequence.

[0349] In one embodiment, an INTERCEPT 429 protein contains a signalsequence corresponding to the portion of the protein from amino acidresidue 1 to about amino acid residue 22 of SEQ ID NO: 153 (SEQ ID NO:154). It is recognized that the carboxyl terminal boundary of the signalsequence can be located one or two residues from the residue identifiedabove (i.e., following residues 20, 21, 22, 23, or 24 of SEQ ID NO:153). The signal sequence is cleaved during processing of the matureprotein.

[0350] INTERCEPT 429 proteins include two transmembrane domains, a pairof extra-membrane domains that flank the cell membrane on the same sideof the membrane, and another extra-membrane domain that flanks the cellmembrane on the opposite side of the membrane. The two transmembranedomains correspond to about amino acid residues 32 to 49 and 59 to 82 ofSEQ ID NO: 153 (i.e., the transmembrane domains having the sequences SEQID NOs: 157 and 159). The pair of extra-membrane domains corresponds toabout amino acid residues 23 to 31 and 83 to 115 of SEQ ID NO: 153(these domains having the sequences SEQ ID NOs: 156 and 160). The otherextra-membrane domain corresponds to about amino acid residues 50 to 58of SEQ ID NO: 153 (this domain having the sequence SEQ ID NO: 158). Inone embodiment, the pair of extra-membrane domains (i.e., those havingthe sequences SEQ ID NOs: 156 and 160) are intracellular domains and theother domain is an extracellular domain. However, in an alternativeform, the pair of extra-membrane domains are extracellular and the otherdomain is cytoplasmic.

[0351] INTERCEPT 429 proteins typically comprise a variety of potentialpost-translational modification sites and protein domains (oftenpositioned within an extracellular or protein surface domain), such asthose described herein in Table VIII, as predicted by computerizedsequence analysis of INTERCEPT 429 proteins using amino acid sequencecomparison software (comparing the amino acid sequence of INTERCEPT 429with the information in the PROSITE database {rel. 122; February, 1995}and the Hidden Markov Models database {Rel. PFAM 3.3}). TABLE VIII AminoType of Potential Modification Site Acid Residues Amino Acid or Domainof SEQ ID NO: 153 Sequence N-glycosylation site 88 to 91 NRSA Caseinkinase II phosphorylation site 93 to 96 TKCD

[0352] In various embodiments, the protein of the invention has one orboth of the post-translational modification sites and domains describedherein in Table VIII.

[0353]FIG. 14B depicts a hydrophobicity plot of human INTERCEPT 429protein. Relatively hydrophobic regions are above the dashed horizontalline, and relatively hydrophilic regions are below the dashed horizontalline. The hydrophobic region which corresponds to amino acid residues 1to 22 of SEQ ID NO: 153 is the signal sequence of human INTERCEPT 429(SEQ ID NO: 154). As described elsewhere herein, relatively hydrophilicregions are generally located at or near the surface of a protein, andare more frequently effective immunogenic epitopes than are relativelyhydrophobic regions. For example, the region of human INTERCEPT 429protein from about amino acid residue 85 to about amino acid residue 100appears to be located at or near the surface of the protein.

[0354] The predicted molecular weight of human INTERCEPT 429 proteinwithout modification and prior to cleavage of the signal sequence isabout 13.4 kilodaltons. The predicted molecular weight of the maturehuman INTERCEPT 429 protein without modification and after cleavage ofthe signal sequence is about 10.8 kilodaltons.

[0355] Expressed sequence tags (ESTs) which exhibit homology with SEQ IDNO: 151 have been isolated from murine small intestine tissue and frompooled human fetal lung, testis, and B cell tissues.

[0356] Uses of INTERCEPT 429 Nucleic Acids,

[0357] Polypeptides, and Modulators Thereof

[0358] INTERCEPT 429 proteins are involved in disorders which affectboth tissues in which they are normally expressed and tissues in whichthey are normally not expressed. Based on the observations that cDNAcorresponding to INTERCEPT 429 occurs in a human heart cDNA library, andthat ESTs obtained from small intestine and one or more of fetal lung,testis, and B cell tissues exhibit homology with MANGO 419 cDNA, it isevident that INTERCEPT 429 protein can be involved in one or morebiological processes which occur in these tissues. In particular,INTERCEPT 429 is involved in modulating growth, proliferation, survival,differentiation, and activity of cells of these tissues (e.g., cardiacmuscle cells), both in normal (i.e., non-diseased) tissues and intissues which are affected by one or more disorders. Examples ofdisorders with which INTERCEPT 429 protein can be associated aredescribed in the following paragraphs.

[0359] Heart disorders with one or more of which INTERCEPT 429 proteinsand nucleic acids can be involved include the cardiovascular disordersdescribed elsewhere in this disclosure. INTERCEPT 429 proteins, nucleicacids encoding them, and agents that modulate activity or expression ofeither of these can be used to prognosticate, diagnose, and treat one ormore of these disorders.

[0360] Muscular disorders in which INTERCEPT 429 proteins and nucleicacids can have a role include muscular dystrophies, myotonic myopathies,glycogen storage disorders and familial periodic paralysis. INTERCEPT429 proteins, nucleic acids encoding them, and agents that modulateactivity or expression of either of these can be used to prognosticate,diagnose, and treat one or more of these disorders.

[0361] Lung disorders with which INTERCEPT 429 proteins and nucleicacids can be associated include, by way of example, asthma, chronic andacute bronchitis, chronic airway obstructive disorders, pulmonaryembolism, pneumonia, and genesis and metastasis of lung tumors.INTERCEPT 429 proteins, nucleic acids encoding them, and agents thatmodulate activity or expression of either of these can be used toprognosticate, diagnose, and treat one or more of these disorders.

[0362] Testicular disorders which can involve INTERCEPT 429 proteins andnucleic acids include, for example, epididymo-orchitis, mumps orchitis,and genesis and metastasis of testicular cancers. INTERCEPT 429proteins, nucleic acids encoding them, and agents that modulate activityor expression of either of these can be used to prognosticate, diagnose,and treat one or more of these disorders.

[0363] B cell disorders in which INTERCEPT 429 proteins and nucleicacids can be involved include leukemias, lymphomas, leukopenias, plasmacell dyscrasias, and splenomegaly. INTERCEPT 429 proteins, nucleic acidsencoding them, and agents that modulate activity or expression of eitherof these can be used to prognosticate, diagnose, and treat one or moreof these disorders.

[0364] TANGO 210

[0365] A cDNA clone (designated jthke034a06) encoding at least a portionof human TANGO 210 protein was isolated from a human fetal skin cDNAlibrary. A corresponding murine cDNA clone (designated jtmMa065g07) wasisolated from a long term bone marrow cDNA library. The ‘long term’ bonemarrow cDNA library was made by reverse transcription of mRNA obtainedfrom bone marrow cells which were cultured for a period (generally twoweeks) prior to stimulating the cells using yeast hyphae and thereafterobtaining mRNA from the cells. Human TANGO 210 protein is predicted bystructural analysis to be a secreted protein although, in an alternativeform, human TANGO 210 protein has a transmembrane region located nearits carboxyl terminal end. Murine TANGO 210 protein is a secretedprotein.

[0366] The full length of the cDNA encoding human TANGO 210 protein(FIG. 15; SEQ ID NO: 171) is 1684 nucleotide residues. The open readingframe (ORF) of this cDNA, nucleotide residues 45 to 1583 of SEQ ID NO:171 (i.e., SEQ ID NO: 172), encodes a 513-amino acid residue protein(FIG. 15; SEQ ID NO: 173), corresponding to a 496-residue secretedprotein.

[0367] The invention thus includes purified human TANGO 210 protein,both in the form of the immature 513 amino acid residue protein (SEQ IDNO: 173) and in the form of the mature 496 amino acid residue protein(SEQ ID NO: 175). Mature human TANGO 210 protein can be in its secretedor membrane-bound form, as described below. The invention also includespurified murine TANGO 210 protein, both in the form of the immature511-amino acid residue protein (SEQ ID NO: 183) and in the form of themature 494-amino acid residue protein (SEQ ID NO: 185). Mature human ormurine TANGO 210 proteins can be synthesized without the signal sequencepolypeptide at the amino terminus thereof, or they can be synthesized bygenerating immature TANGO 210 protein and cleaving the signal sequencetherefrom.

[0368] The invention includes nucleic acid molecules which encode apolypeptide of the invention. Such nucleic acids include, for example, aDNA molecule having the nucleotide sequence listed in SEQ ID NO: 171 orsome portion thereof or SEQ ID NO: 181 or some portion thereof, such asthe portion which encodes mature human or murine TANGO 210 protein,immature human or murine TANGO 210 protein, or a domain of human ormurine TANGO 210 protein. These nucleic acids are collectively referredto as nucleic acids of the invention.

[0369] TANGO 210 proteins and nucleic acid molecules encoding themcomprise a family of molecules having certain conserved structural andfunctional features.

[0370] A common domain present in TANGO 210 proteins is a signalsequence. In one embodiment, a TANGO 210 protein contains a signalsequence corresponding to the portion of the protein from amino acidresidue 1 to about amino acid residue 17 of SEQ ID NO: 173 (SEQ ID NO:174) or to the portion of the protein from amino acid residue 1 to aboutamino acid residue 17 of SEQ ID NO: 183 (SEQ ID NO: 184). It isrecognized that the carboxyl terminal boundary of the signal sequencecan be located one or two residues from the residue identified above(i.e., at residue 15, 16, 17, 18, or 19 of SEQ ID NO: 173 or at residue15, 16, 17, 18, or 19 of SEQ ID NO: 183). The signal sequence is cleavedduring processing of the mature protein.

[0371] TANGO 210 proteins can also include an extracellular domain.Murine TANGO 210 protein is secreted. However, in one alternative form,the human TANGO 210 protein is a transmembrane protein having anextracellular domain located from about amino acid residue 25 to aminoacid residue 488 of SEQ ID NO: 173 (i.e., SEQ ID NO: 178). In thisalternative form, human TANGO 210 protein also has a transmembraneregion (i.e., about amino acid residues 489 to 506 of SEQ ID NO: 173;SEQ ID NO: 179) and an intracellular domain (i.e., about amino acidresidues 507 to 513 of SEQ ID NO: 173; SEQ ID NO: 180). In anotheralternative form, human TANGO 210 protein has an intracellular domainlocated from about amino acid residue 25 to amino acid residue 488 ofSEQ ID NO: 173 (i.e., SEQ ID NO: 178), a transmembrane region (i.e.,about amino acid residues 489 to 506 of SEQ ID NO: 173; SEQ ID NO: 179),and an extracellular domain (i.e., about amino acid residues 507 to 513of SEQ ID NO: 173; SEQ ID NO: 180).

[0372] TANGO 210 proteins typically comprise a variety of potentialpost-translational modification sites (often within an extracellulardomain), domains, or both, such as those described herein in Tables IX(for human TANGO 210) and X (for murine TANGO 210), as predicted bycomputerized sequence analysis of TANGO 210 proteins using amino acidsequence comparison software (comparing the amino acid sequence of TANGO210 with the information in the PROSITE database {rel. 12.2; February1995} and the Hidden Markov Models database {Rel. PFAM 3.3}). TABLE IXAmino Acid Residues Type of Potential Modification Site of SEQ AminoAcid or Domain ID NO: 173 Sequence N-glycosylation site 55 to 58 NRSL110 to 113 NLTY 200 to 203 NWTK 452 to 455 NITR 470 to 473 NSSF 508 to511 NTSI Protein kinase C phosphorylation site 75 to 77 TGK 88 to 90 TPR112 to 114 TYR 290 to 292 TFR 384 to 386 TTR 422 to 424 SIR Caseinkinase II phosphorylation site 24 to 27 TENE 57 to 60 SLID 193 to 196THFD 249 to 252 SQDD 311 to 314 TDVE N-myristoylation site 71 to 76GLTVTG 205 to 210 GAGFNL 223 to 228 GLSHSN Hemopexin domain signature318 to 333 See FIG. 15 Hemopexin domain 285 to 327 See FIG. 15 329 to371 376 to 423 425 to 465 Peptidase_M10 domain  36 to 202 See FIG. 15Neutral zinc metallopeptidase zinc- 213 to 222 See FIG. 15 bindingdomain signature Matrix metalloprotease cysteine switch 89 to 96PRCGVPDV

[0373] TABLE X Amino Acid Type of Potential Modification Site ResiduesAmino Acid or Domain of SEQ ID NO: 183 Sequence N-glycosylation site  55to 58 NRSL 453 to 456 NITQ 471 to 474 NASF 475 to 478 NVSV cAMP- orcGMP-dependent protein 107 to 110 RKYS kinase phosphorylation site 493to 496 KRLS Protein kinase C phosphorylation site  75 to 77 TGK 112 to114 TYR 268 to 270 TTK 291 to 293 TFR 336 to 338 SPR 386 to 388 TRK 477to 479 SVK Casein kinase II phosphorylation site  57 to 60 SLFD 123 to126 TPAD 193 to 196 THFD 250 to 253 SQDD 336 to 339 SPRDN-myristoylation site  71 to 76 GLTVTG  86 to 191 GLGLGG 224 to 229GLSHSN Hemopexin domain signature 319 to 334 See FIG. 15 Hemopexindomain 286 to 328 See FIG. 15 330 to 372 377 to 424 426 to 466Zinc-binding metallopeptidase_M10  36 to 202 See FIG. 15 domain Neutralzinc metallopeptidase zinc- 214 to 223 See FIG. 15 binding domainsignature Matrix metalloproteinase cysteine  89 to 96 PRCGVPDV switch

[0374] In various embodiments, the protein of the invention has at least1, 2, 4, 6, 10, 15, or 20 or more of the post-translational modificationsites described herein in Tables 1× and X.

[0375] Examples of additional domains present in human and murine TANGO210 protein include hemopexin domains and peptidase_M10 domains andsignature sequences corresponding to hemopexin domains, zinc-bindingdomains, and matrix metalloproteinase (MMP) cysteine switches. In oneembodiment, the protein of the invention has at least one domain orsignature sequence that is at least 55%, preferably at least about 65%,more preferably at least about 75%, yet more preferably at least about85%, and most preferably at least about 95% identical to one of thedomains and signature sequences described herein in Tables 1× and X.Preferably, the protein of the invention has at least one hemopexindomain, one peptidase_M10 domain, one hemopexin domain signaturesequence, one zinc-binding domain signature sequence, and one MMPcysteine switch signature sequence.

[0376] Hemopexin domains derive their name from a portion of a proteindesignated hemopexin. Hemopexin is a serum glycoprotein that binds withheme and transports it to the liver. Hemopexin domains facilitatebinding of the protein comprising the domain with a variety of moleculesand other proteins. Besides hemopexin, hemopexin domains occur in MMPsand in vitronectin, a cell adhesion and factor (Hunt et al. (1987) Prot.Seq. Data Anal. 1:21-26; Stanley (1986) FEBS Lett. 199:249-253. Aconsensus hemopexin domain signature sequence has been identified (PfamAccession PDOC00023), which has the structure

[0377] (L, I, A, or T)-X₃—W-X(₂ or ₃)—(P or E)-X₂-(L, I, V, M, F, orY)-(D, E, N, Q, or S)—(S, T, or A)-(A or V)-(L, I, V, M, F, or Y), (SEQID NO: 451)

[0378] wherein standard single-letter amino acid codes are used, X beingany amino acid residue. Each of the human and murine TANGO 210 aminoacid sequences include a single copy of this consensus sequence. Thisconsensus sequence occurs in the amino acid sequences of many MMPs,including MMPs-1, -2, -3, -9, -10, -11, -12, -14, -15, and -16.

[0379] Peptidase_M 10 domains are conserved amino acid sequences whichoccur in type 10 zinc-dependent metalloproteinases, according to theclassification of Rawlings et al. (1995, Meth. Enzymol 248:183-228).Several mammalian MMPs are type 10 zinc-dependent metalloproteinasesincluding, for example, MMP-1 (interstitial collagenase), MMP-2 (72kilodalton gelatinase), MMP-3 (stromelysin-1) MMP-7 (matrylisin), MMP-8(neutrophil collagenase), MMP-9 (92 kilodalton gelatinase), and MMP-10(stromelysin-2; Woessner, 1991, FASEB J. 5:2145-2154). The peptidase_M10domain includes a consensus zinc-binding domain signature sequencehaving the structure

[0380] (G, S, T, A, L, I, V, or N)—X₂—H-E-(L, I, V, M, F, Y, or W)-(D,E, G, H, R, K, or P)—H—X-(L, I, V, M, F, Y, W, G, S, P, or Q), (SEQ IDNO: 452)

[0381] wherein standard single-letter amino acid codes are used, X beingany amino acid residue. The two histidine residues of the consensussequence have been recognized as zinc ligands, and the glutamate residueis the (proteinase) active site residue. Each of the human and murineTANGO 210 amino acid sequences include this consensus sequence.

[0382] Another distinguishing characteristic of mammalian extracellularMMPs is presence in the amino acid sequence of the MMP of an MMPcysteine switch signature. The consensus MMP cysteine switch signaturesequence has the structure

[0383] P—R—C-(G or N)—X—P-(D or R)-(L, I, V, S, A, P, K, or Q) (SEQ IDNO: 453)

[0384] wherein standard single-letter amino acid codes are used, X beingany amino acid residue. Each of the human and murine TANGO 210 aminoacid sequences include a single copy of this consensus sequence. HumanMMPs in which this consensus sequence occurs include MMPs-1, -2, -3, -7,-8, -9, -10, -11, -12, -13, -14, -15, and -16.

[0385] The signal peptide prediction program SIGNALP (Nielsen et al.(1997) Protein Engineering 10:1-6) predicted that human TANGO 210protein includes an approximately 17 amino acid signal peptide (aminoacid residues 1 to 15, 16, 17, 18, or 19 of SEQ ID NO: 173; SEQ ID NO:174) preceding the mature, secreted TANGO 210 protein (amino acidresidues 18 to 513 of SEQ ID NO: 173; SEQ ID NO: 175). In onealternative form, human TANGO 210 protein includes an extracellulardomain (amino acid residues 18 to 488 of SEQ ID NO: 173; SEQ ID NO:178), a transmembrane domain (amino acid residues 489 to 506 of SEQ IDNO: 173; SEQ ID NO: 179), and a cytoplasmic domain (amino acid residues507 to 513 of SEQ ID NO: 173; SEQ ID NO: 180). In another alternativeform, human TANGO 210 protein includes a cytoplasmic domain (amino acidresidues 18 to 488 of SEQ ID NO: 173; SEQ ID NO: 178), a transmembranedomain (amino acid residues 489 to 506 of SEQ ID NO: 173; SEQ ID NO:179), and an extracellular domain (amino acid residues 507 to 513 of SEQID NO: 173; SEQ ID NO: 180).

[0386]FIG. 15E depicts a hydrophobicity plot of human TANGO 210 protein.

[0387] Relatively hydrophobic regions are above the dashed horizontalline, and relatively hydrophilic regions are below the dashed horizontalline. The hydrophobic region which corresponds to amino acid residues 1to about 17 of SEQ ID NO: 173 is the signal sequence of human TANGO 210(SEQ ID NO: 174). The hydrophobic region which corresponds to amino acidresidues 489 to 506 of SEQ ID NO: 173 is the transmembrane portion inthe alternative form of human TANGO 210 protein. As described elsewhereherein, relatively hydrophilic regions are generally located at or nearthe surface of a protein, and are more frequently effective immunogenicepitopes than are relatively hydrophobic regions. For example, theregion of human TANGO 210 protein from about amino acid residue 190 toabout amino acid residue 205 appears to be located at or near thesurface of the protein, while the region from about amino acid residue145 to about amino acid residue 155 appears not to be located at or nearthe surface.

[0388] The predicted molecular weight of human TANGO 210 protein withoutmodification and prior to cleavage of the signal sequence is about 59.0kilodaltons. The predicted molecular weight of the mature human TANGO210 protein without modification and after cleavage of the signalsequence is about 57.0 kilodaltons.

[0389] Northern hybridization experiments using human tissue samplesindicated that mRNA corresponding to the cDNA encoding TANGO 210 isexpressed in the tissues listed in Table XI, wherein “+” indicatesdetectable expression and “−” indicates failure to detect expression.TABLE XI Animal Tissue Expression Human kidney + (Adult) heart − brain −placenta − lung − liver − skeletal muscle − pancreas − Human kidney +(Fetus)

[0390] Human TANGO 210 exhibits sequence similarity to human MMP-8(GENBANK™ Accession No. J05556), as indicated herein in FIGS. 15V and15W, which list an alignment of the amino acid sequences of theseproteins. FIGS. 15X-1 through 15X-6 depict an alignment of thenucleotide sequences of the ORFs of human TANGO 210 (SEQ ID NO: 172) andMMP-8 (SEQ ID NO: 176). In these alignments (each made using the ALIGNsoftware; pam120.mat scoring matrix; gap penalties −12/−4), the aminoacid and ORF nucleotide sequences corresponding to these two proteinsare 43.9% identical and 57.1% identical, respectively.

[0391] The full length of the cDNA encoding murine TANGO 210 protein(FIG. 15; SEQ ID NO: 181) is 2467 nucleotide residues. The ORF of thiscDNA, nucleotide residues 22 to 927 and about 1280 to 1906 of SEQ ID NO:181 (i.e., collectively, SEQ ID NO: 182), encodes a 510-amino acidresidue protein (FIG. 15; SEQ ID NO: 183). It is recognized that theprecise locations of the intron boundaries in SEQ ID NO: 181 have notbeen identified. Thus, murine TANGO 210 protein can comprise one or moreadditional or one or more fewer amino acid residues at the exon-exonboundary (i.e., between about residues 302 and 303 of SEQ ID NO: 183).

[0392] The signal peptide prediction program SIGNALP (Nielsen et al.(1997) Protein Engineering 10:1-6) predicted that murine TANGO 210protein includes an approximately 17 amino acid signal peptide (aminoacid residues 1 to about 17 of SEQ ID NO: 183; SEQ ID NO: 184) precedingthe mature TANGO 210 protein (amino acid residues 18 to 511 of SEQ IDNO: 183; SEQ ID NO: 185). Murine TANGO 210 protein is a secretedprotein.

[0393]FIG. 15J depicts a hydrophobicity plot of murine TANGO 210protein.

[0394] Relatively hydrophobic regions are above the dashed horizontalline, and relatively hydrophilic regions are below the dashed horizontalline. The hydrophobic region which corresponds to amino acid residues 1to about 17 of SEQ ID NO: 183 is the signal sequence of murine TANGO 210(SEQ ID NO: 184). As described elsewhere herein, relatively hydrophilicregions are generally located at or near the surface of a protein, andare more frequently effective immunogenic epitopes than are relativelyhydrophobic regions. For example, the region of murine TANGO 210 proteinfrom about amino acid residue 18 to about amino acid residue 28 appearsto be located at or near the surface of the protein, while the regionfrom about amino acid residue 148 to about amino acid residue 158appears not to be located at or near the surface

[0395] The predicted molecular weight of murine TANGO 210 proteinwithout modification and prior to cleavage of the signal sequence isabout 58.7 kilodaltons. The predicted molecular weight of the maturemurine TANGO 210 protein without modification and after cleavage of thesignal sequence is about 56.2 kilodaltons.

[0396] Human and murine TANGO 210 proteins exhibit considerable sequencesimilarity, as indicated herein in FIGS. 15K and 15L. FIGS. 15K and 15Ldepict an alignment of human and murine TANGO 210 amino acid sequences(SEQ ID NOs: 173 and 183, respectively). In this alignment (made usingthe ALIGN software {Myers and Miller (1989) CABIOS, ver. 2.0};pam120.mat scoring matrix; gap penalties −12/−4), the proteins are 77.2%identical in the overlapping region (i.e., 393 identical residues out of509 residues in the overlapping region, which includes amino acidresidues 1-509 of SEQ ID NO: 173 and amino acid residues 1-509 of SEQ IDNO: 183). The human and murine cDNAs encoding TANGO 210 are 76.2%identical in the overlapping portions (i.e., nucleotide residues 29-1601of SEQ ID NO: 171 and nucleotide residues 8-927 and 1280-1935 of SEQ IDNO: 181), as assessed using the same software and parameters and asindicated in FIGS. 15M through 15U. In the respective ORFs, SEQ ID NOs:171 and 181 are 81.7% identical.

[0397] Human TANGO 210 Gene Expression Analysis

[0398] Expression of TANGO 210 in selected human tissues and cell typeswas analyzed as follows. Total RNA was prepared from selected humantissues using a single step extraction method using the RNA STAT-60™ kitaccording to the manufacturer's instructions (TelTest, Inc). Each RNApreparation was treated with DNase I (Ambion) at 37° C. for 1 hour.DNase I treatment was considered to be complete if the sample requiredat least 38 PCR amplification cycles to reach a threshold level offluorescence using β-2 microglobulin as an internal amplicon reference.The integrity of the RNA samples following DNase I treatment wasconfirmed by agarose gel electrophoresis and ethidium bromide staining.Following phenol extraction, cDNA was prepared from the sample using theSUPERSCRIP™ Choice System following the manufacturer's instructions(Gibco BRL). A negative control of RNA without reverse transcriptase wasmock reverse-transcribed for each RNA sample.

[0399] TANGO 210 expression was measured by TAQMAN® quantitative PCR(Perkin Elmer Applied Biosystems) in cDNA prepared from the followingnormal human tissues: prostate, liver, breast, skeletal muscle, brain,colon, heart, ovary, kidney, lung, vein, aorta, testis, thyroid,placenta, fetal liver, fetal heart, osteoblasts (undifferentiated),small intestine, spleen, thymus, and lymph node. Probes were designed byPRIMEREXPRESS™ software (PE Biosystems) based on the sequence of eachgene.

[0400] Each gene probe was labeled using FAM (6-carboxyfluorescein), andthe β2-microglobulin reference probe was labeled with a differentfluorescent dye, VIC. The differential labeling of the target gene andinternal reference gene thus enabled measurement in same well. Forwardand reverse primers and the probes for both P2-microglobulin and targetgene were added to the TAQMAN® Universal PCR Master Mix (PE AppliedBiosystems). Although the final concentration of primer and probevaried, each was internally consistent within a given experiment. Atypical experiment contained 200 nanomolar forward and reverse primersand 100 nanomolar probe for β-2 microglobulin, and 600 nanomolar forwardand reverse primers and 200 nanomolar probe for the target gene. TAQMAN®matrix experiments were carried out using an ABI PRISM™ 7700 SequenceDetection System (PE Applied Biosystems). The thermal cycler conditionswere as follows: hold for 2 minutes at 50° C. and 10 minutes at 95° C.,followed by two-step PCR for 40 cycles of 95° C. for 15 seconds followedby 60° C. for 1 minute.

[0401] The following method was used to quantitatively calculate TANGO210 gene expression in the selected tissues relative to P-2microglobulin expression in the same tissue. The threshold cycle (Ct)value is defined as the cycle at which a statistically significantincrease in fluorescence is detected. A lower Ct value is indicative ofa higher mRNA concentration. The Ct value of the kinase gene isnormalized by subtracting the Ct value of the β-2 microglobulin gene toobtain a ΔCt value using the following formula: ΔCt=Ct_(kinase)−Ct_(β-2)microglobulin. Expression is then calibrated against a cDNA sampleshowing a comparatively low level of expression of the kinase gene. TheΔCt value for the calibrator sample is then subtracted from ΔCt for eachtissue sample according to the following formula:ΔΔCt=ΔCt−_(sample)-ΔCt−_(calibrator). Relative expression is thencalculated using the arithmetic formula given by 2^(−ΔΔCt) Expression ofthe target gene in each of the tissues tested is then graphicallyrepresented as discussed in more detail below.

[0402]FIG. 15Y depicts expression of TANGO 210 in various tissues andcell lines as described above, relative to expression in fetal hearttissue. The results indicate significant expression in breast, skeletalmuscle, colon, vein, aorta, testis, thyroid, and small intestinetissues.

[0403] Uses of TANGO 210 Nucleic Acids,

[0404] Polypeptides, and Modulators Thereof

[0405] TANGO 210 proteins are involved in disorders which affect bothtissues in which they are normally expressed and tissues in which theyare normally not expressed. Based on the observations that cDNAcorresponding to TANGO 210 occurs in a human fetal skin cDNA library andin a murine long term bone marrow cDNA library, and that RNAcorresponding to TANGO 210 is detectable by Northern analysis of humanadult and fetal kidney tissue, it is evident that TANGO 210 protein isinvolved in one or more biological processes which occur in thesetissues. In particular, TANGO 210 is involved in modulating one or moreof growth, proliferation, survival, differentiation, activity,morphology, and movement/migration of cells of these tissues. TANGO 210is involved in modulating the structure of extracellular matrix whichcontacts or is in fluid communication with cells of these tissues. Thus,TANGO 210 has a role in disorders which affect these cells and one ormore of their growth, proliferation, survival, differentiation,activity, morphology, and movement/migration, as well as the biologicalfunction of organs comprising one or more of these tissues.

[0406] The Northern analysis data described herein for human TANGO 210indicate that nucleic acids corresponding to (i.e., homologous with orcomplementary to) all or part of human TANGO 210 cDNA or molecules(e.g., antibodies) which react specifically with human TANGO 210 proteinor a portion thereof can be used to identify kidney tissue or todifferentiate kidney tissue from other types of tissue, such as heart,brain, placenta, lung, liver, and pancreas tissues. Thus, human TANGO210 proteins, nucleic acids, and compounds which interact specificallywith either of these, can be used for one or more of tissue typing,identification, and separation.

[0407] TANGO 210 gene expression data described herein indicate thatTANGO 210 can be expressed in at least breast, skeletal muscle, colon,vein, aorta, testis, thyroid, small intestine, and spleen tissues. Thus,TANGO 210 can have a role in disorders which affect cells of thesetissues and one or more of their growth, proliferation, survival,differentiation, activity, morphology, and movement/migration, as wellas the biological function of organs comprising one or more of thesetissues.

[0408] The fact that TANGO 210 is expressed in breast tissue is anindication that TANGO 210 can be involved in both normal physiologicalfunction of breast tissue and in breast disorders. Examples of breastdisorders include breast cancer, insufficient lactation, infantnutritional and growth disorders, mastalgia, fibroadenomas, breastinfections, and gynecomastia.

[0409] In another example, TANGO 210 polypeptides, nucleic acids, andmodulators thereof, can be involved in normal and aberrant functioningof skeletal muscle tissue, and can thus be involved in disorders of suchtissue. Examples of skeletal muscle disorders include muscular dystrophy(e.g., Duchenne muscular dystrophy, Becker muscular dystrophy,Emery-Dreifuss muscular dystrophy, limb-girdle muscular dystrophy,facioscapulohumeral muscular dystrophy, myotonic dystrophy,oculopharyngeal muscular dystrophy, distal muscular dystrophy, andcongenital muscular dystrophy), motor neuron diseases (e.g., amyotrophiclateral sclerosis, infantile progressive spinal muscular atrophy,intermediate spinal muscular atrophy, spinal bulbar muscular atrophy,and adult spinal muscular atrophy), myopathies (e.g., inflammatorymyopathies (e.g., dermatomyositis and polymyositis), myotonia congenita,paramyotonia congenita, central core disease, nemaline myopathy,myotubular myopathy, and periodic paralysis), and metabolic diseases ofmuscle (e.g., phosphorylase deficiency, acid maltase deficiency,phosphofructokinase deficiency, de-brancher enzyme deficiency,mitochondrial myopathy, carnitine deficiency, carnitine palmityltransferase deficiency, phosphoglycerate kinase deficiency,phosphoglycerate mutase deficiency, lactate dehydrogenase deficiency,and myoadenylate deaminase deficiency). TANGO 210 polypeptides, nucleicacids, or modulators thereof can be used to prognosticate, diagnose,inhibit, prevent, or alleviate one or more of these disorders.

[0410] In another example, TANGO 210 polypeptides, nucleic acids, andmodulators thereof can be used to treat colonic disorders, such as thosedescribed elsewhere in this disclosure.

[0411] In another example, TANGO 210 polypeptides, nucleic acids, andmodulators thereof, can be used to treat cardiovascular disorders, suchas those described elsewhere in this disclosure.

[0412] In another example, TANGO 210 polypeptides, nucleic acids, ormodulators thereof, can be used to treat testicular disorders, such asthose described elsewhere in this disclosure.

[0413] TANGO 210 polypeptides, nucleic acids, and modulators thereof,can be involved in disorders of the thyroid gland, such ashyperthyroidism (e.g., diffuse toxic hyperplasia, toxic multi-nodulargoiter, toxic adenoma, and acute or sub-acute thyroiditis),hypothyroidism (e.g., cretinism and myxedema), thyroiditis (e.g.,Hashimoto's thyroiditis, sub-acute granulomatous thyroiditis, sub-acutelymphocytic thyroiditis, Riedel's thryroiditis), Graves' disease, goiter(e.g., simple diffuse goiter and multi-nodular goiter), and tumors(e.g., adenoma, papillary carcinoma, follicular carcinoma, medullarycarcinoma, undifferentiated malignant carcinoma, Hodgkin's disease, andnon-Hodgkin's lymphoma). TANGO 210 polypeptides, nucleic acids, ormodulators thereof can be used to prognosticate, diagnose, inhibit,prevent, or alleviate one or more of these disorders.

[0414] In another example, TANGO 210 polypeptides, nucleic acids, andmodulators thereof can be used to treat intestinal disorders (e.g.,disorders of the small intestine), such as ischemic bowel disease,infective enterocolitis, Crohn's disease, benign tumors, malignanttumors (e.g., argentaffinomas, lymphomas, adenocarcinomas, andsarcomas), malabsorption syndromes (e.g., celiac disease, tropicalsprue, Whipple's disease, and abetalipoproteinemia), obstructivelesions, hernias, intestinal adhesions, intussusception, and volvulus.

[0415] TANGO 210 nucleic acids, proteins, and modulators thereof can beused to modulate proliferation, migration, morphology, differentiation,function, or some combination of these, of cells that form the spleen,(e.g., cells of the splenic connective tissue, splenic smooth muscletells, or endothelial cells of the splenic blood vessels) or of bloodcells that are processed (e.g., regenerated, matured, or phagocytized)within the spleen, as described elsewhere in this disclosure.

[0416] There are several indications that TANGO 210 is an MMP. Forinstance, presence of each of a Peptidase_M110 domain, a zinc-bindingdomain signature, a hemopexin domain signature, and a cysteine switch inthe amino acid sequences of both human and murine TANGO 210 indicatesthat TANGO 210 exhibits extracellular matrix proteinase activity (e.g.,collagenase and basement membrane degradative activities). In addition,homology between the sequence of human TANGO 210 and MMPs (e.g., MMP-8,as described herein) is a further indication the TANGO 210 is an MMP.

[0417] MMPs degrade extracellular matrix (ECM), and are thus involved inmaintenance, and in renewal and replacement of old ECM with new ECM. ECMserves numerous purposes in the body, including providing support,containment, or both, to specialized tissues (e.g., tissues of organssuch as skin, kidney, bone marrow, etc.) and regulating fluid balance intissues which line a void or fluid-filled compartment (e.g., skin,bladder, kidney, stomach, etc.). Demonstration, as described herein,that TANGO 210 is expressed in several of these tissues (fetal skin,bone marrow, kidney) indicates that TANGO 210 is involved in one or moreof these processes.

[0418] An important function of kidney tissue is to regulate the volumeand composition of body fluids. The kidneys regulate body fluids byselectively permitting water, electrolytes, metabolites, and the like topass from the plasma into the bladder in a regulatable manner whileretaining cells and proteins in the plasma. By regulating fluid balance,the kidneys also exert a significant effect on arterial blood pressure.The kidneys perform these functions in a manner analogous to filtration.

[0419] Fluid outflow from the plasma occurs through the membranes ofkidney glomerular capillaries in structures designated Bowman'scapsules. The membrane of glomerular capillaries has three layers(normal capillaries have only two). Glomerular capillaries have a highlyfenestrated luminal endothelium which can serve to prevent passage ofcells through the capillary membrane, but do not substantially inhibitpassage of serum proteins. Surrounding the endothelium is an ECMbasement membrane comprising collagen and peptidoglycan. An epitheliallayer having gaps or channels through which glomerular filtrate ispassed surrounds the basement membrane.

[0420] The basement membrane is the layer of the glomerular capillarymembrane which is principally responsible for retention of serumproteins. In order to maintain proper operation of the kidneys, it iscritical that the relative porosity of the basement membrane bemaintained. Mineral precipitates, circulating bacteria, and the like canclog the pores of the basement membrane. Turnover, renewal, orcontrolled degradation of the basement membrane ensures that thebasement membrane remains functional. TANGO 210 is involved inregulating the thickness, porosity, and rate of degradation of thebasement membrane of glomerular capillaries and other ECM components ofkidney tissue. TANGO 210 is therefore involved in normal and abnormalformation and maintenance of functional kidney tissue. Thus, TANGO 210is involved in a number of disorders which relate to aberrant kidneytissue formation and function. Such disorders include the kidneydisorders described elsewhere herein. TANGO 210 proteins, nucleic acidsencoding them, and agents that modulate activity or expression of eitherof these can be used to prognosticate, diagnose, treat, and inhibit oneor more of these disorders.

[0421] Recovery of a cDNA encoding TANGO 210 from a murine long termbone marrow cDNA library indicates that TANGO 210 is expressed in bonemarrow, and is thus involved both in normal physiological processeswhich occur in bone marrow and in disorders which affect bone marrow.ECM is a significant component of bone marrow, and TANGO 210 is involvedin degradation of ECM associated with turnover/renewal of bone marrowtissue, and with changes which occur in the bone marrow with age. Asmammals age, the bone marrow becomes increasingly gelatinous and the ECMcomposition of the marrow changes. The cellular content of the bonemarrow changes with time as well. In young mammals, most bones arefilled with red marrow, which comprises large numbers of hematopoieticcells. As mammals age, red marrow is replaced by gelatinous, adiposecell-containing white and yellow marrows. TANGO 210 is involved in ECMchanges which accompany age related changes in marrow composition. TANGO210 is also involved in bone marrow-related disorders such as bonemarrow failure (e.g., that associated with anemia) and rejection ofheterologous implanted bone marrow. TANGO 210 proteins, nucleic acidsencoding them, and agents that modulate activity or expression of eitherof these can be used to prognosticate, diagnose, treat, and inhibit oneor more of these disorders. In addition, because TANGO 210 is associatedwith remodeling of bone marrow, TANGO 210 is also capable of modulatingacceptance of donor bone marrow in a recipient.

[0422] Recovery of a cDNA encoding TANGO 210 from a human fetal skincDNA library indicates that TANGO 210 is expressed in human skin, and isinvolved both in normal physiological processes which occur in skin andin skin disorders. Skin is a multi-layered tissue in which the varioustissue layers can have different ECM compositions. Skin has a variety ofroles in the normal mammal. Skin maintains the mechanical, osmotic,chemical, photic, and thermal integrity of the exterior surface of themammal. TANGO 210, being expressed in the skin and able to modulate ECMcomposition, is therefore involved in regulating these characteristicsin normal individuals and in individuals afflicted with disordersrelating to aberrant regulation of these characteristics (e.g.,ichthyosis). TANGO 210 is also involved in other disorders which occurin or affect ECM in skin. Such disorders include, by way of example,psoriasis, infections, wounds (and healing of wounds), inflammation,dermatitis, acne, benign and malignant dermatological tumors, and thelike. TANGO 210 proteins, nucleic acids encoding them, and agents thatmodulate activity or expression of either of these can be used toprognosticate, diagnose, treat, and inhibit one or more of thesedisorders.

[0423] Numerous cancers are associated with aberrant MMP expression andactivity. MMPs can aid cancer growth and metastasis by degrading ECM,thereby providing an avenue for angiogenesis, cell growth, or cellmovement through a tissue. TANGO 210 is able to modulate the rate andextent of angiogenesis, and is therefore useful for prognosticating,diagnosing, treating, and inhibiting one or more disorders associatedwith aberrant angiogenesis, including, but not limited to cancers.Disorders associated with aberrant angiogenesis include both thoseassociated with an abnormally high rate or extent of angiogenesis (e.g.,cancerous growth and metastasis) and those associated with an abnormallyor insufficiently low rate or extent of angiogenesis (e.g., impairedwound healing, transplanted tissue rejection, and acute and chronicischemic disorders such as stroke). TANGO 210 proteins, nucleic acidsencoding them, and agents that modulate activity or expression of eitherof these can be used to prognosticate, diagnose, treat, and inhibit oneor more cancers or other disorders associated with aberrantangiogenesis.

[0424] TANGO 366

[0425] A cDNA clone (designated jthqc016c02) encoding at least a portionof human TANGO 366 protein was isolated from a human normal prostatefibroblast cDNA library by SPOT analysis. Human TANGO 366 protein ispredicted by structural analysis to be a transmembrane protein.

[0426] The full length of the cDNA encoding human TANGO 366 protein(FIG. 16; SEQ ID NO: 191) is 2628 nucleotide residues. The ORF of thiscDNA, nucleotide residues 86 to 1144 of SEQ ID NO: 191 (i.e., SEQ ID NO:192), encodes a 353-amino acid residue protein (FIG. 16; SEQ ID NO:193), corresponding to a 337-residue transmembrane protein.

[0427] The invention thus includes purified human TANGO 366 protein,both in the form of the immature 353 amino acid residue protein (SEQ IDNO: 193) and in the form of the mature 337 amino acid residue protein(SEQ ID NO: 195). Mature human TANGO 366 proteins can be synthesizedwithout the signal sequence polypeptide at the amino terminus thereof,or it can be synthesized by generating immature TANGO 366 protein andcleaving the signal sequence therefrom.

[0428] The invention includes nucleic acid molecules which encode apolypeptide of the invention. Such nucleic acids include, for example, aDNA molecule having the nucleotide sequence listed in SEQ ID NO: 191 orsome portion thereof, such as the portion which encodes mature humanTANGO 366 protein, immature human TANGO 366 protein, or a domain ofhuman TANGO 366 protein. These nucleic acids are collectively referredto as nucleic acids of the invention.

[0429] TANGO 366 proteins and nucleic acid molecules encoding themcomprise a family of molecules having certain conserved structural andfunctional features.

[0430] A common domain present in TANGO 366 proteins is a signalsequence. In one embodiment, a TANGO 366 protein contains a signalsequence corresponding to the portion of the protein from amino acidresidue 1 to about amino acid residue 16 of SEQ ID NO: 193 (SEQ ID NO:194). It is recognized that the carboxyl terminal boundary of the signalsequence can be located one or two residues from the residue identifiedabove (i.e., at residue 14, 15, 16, 17, or 18 of SEQ ID NO: 193). Thesignal sequence is cleaved during processing of the mature protein.

[0431] TANGO 366 proteins can include an extracellular domain. The humanTANGO 366 protein extracellular domain is located from about amino acidresidue 17 to amino acid residue 216 of SEQ ID NO: 193 (i.e., theextracellular domain has the sequence SEQ ID NO: 196).

[0432] In addition, TANGO 366 can include a transmembrane domain. In oneembodiment, a TANGO 366 protein of the invention contains atransmembrane domain corresponding to about amino acid residues 217 to239 of SEQ ID NO: 193 (i.e., the transmembrane domain has the sequenceSEQ ID NO: 197).

[0433] The present invention includes TANGO 366 proteins having acytoplasmic domain, particularly including proteins having acarboxyl-terminal cytoplasmic domain. The human TANGO 366 cytoplasmicdomain is located from about amino acid residue 240 to amino acidresidue 353 of SEQ ID NO: 193 (i.e., the cytoplasmic domain has thesequence SEQ ID NO: 198).

[0434] In an alternative embodiment, TANGO 366 proteins can have acytoplasmic domain located from about amino acid residue 17 to aminoacid residue 216 of SEQ ID NO: 193 (i.e., the cytoplasmic domain has thesequence SEQ ID NO: 196); a transmembrane domain corresponding to aboutamino acid residues 217 to 239 of SEQ ID NO: 193 (i.e., thetransmembrane domain has the sequence SEQ ID NO: 197); and anextracellular domain located from about amino acid residue 240 to aminoacid residue 353 of SEQ ID NO: 193 (i.e., the extracellular domain hasthe sequence SEQ ID NO: 198)

[0435] TANGO 366 proteins typically comprise a variety of potentialpost-translational modification sites (often within an extracellulardomain), such as those described herein in Table XII, as predicted bycomputerized sequence analysis of TANGO 366 proteins using amino acidsequence comparison software (comparing the amino acid sequence of TANGO366 with the information in the PROSITE database {rel. 12.2; February1995} and the Hidden Markov Models database {Rel. PFAM 3.3}). TABLE XIIAmino Acid Type of Potential Modification Site Residues Amino Acid orDomain of SEQ ID NO: 193 Sequence N-glycosylation site  74 to 77 NESV137 to 140 NLSH Protein kinase C phosphorylation site  16 to 18 TTR  67to 69 SNR 332 to 334 SPK Casein kinase II phosphorylation site  40 to 43TRVD 280 to 283 SLQE Tyrosine kinase phosphorylation site 318 to 325RLVREGTY N-myristoylation site  13 to 18 GAQTTR  32 to 37 GLFDSF  88 to93 GLDLSH 214 to 219 GNPLAV 223 to 228 GAFAGL Glycosaminoglycanattachment site  45 to 48 SGLG Leucine rich repeat amino terminal  19 to58 See FIG. 16 (LRRNT) domain Leucine rich repeat (LRR) domain  59 to 82See FIG. 16  85 to 108 109 to 132 133 to 155 185 to 206 207 to 229 230to 254 255 to 279 280 to 303 Leucine zipper pattern 284 to 305 See FIG.16

[0436] In various embodiments, the protein of the invention has at least1, 2, 4, 6, 10, 15, or 20 or more of the post-translational modificationsites described herein in Table XII.

[0437] Examples of additional domains present in human TANGO 366 proteininclude a glycosaminoglycan attachment site, several leucine rich repeat(LRR and LRRNT) domains, and a leucine zipper domain. In one embodiment,the protein of the invention has at least one domain that is at least55%, preferably at least about 65%, more preferably at least about 75%,yet more preferably at least about 85%, and most preferably at leastabout 95% identical to one of the LRR or leucine zipper domainsdescribed herein in Table XII. Preferably, the protein of the inventionhas at least one LRR domain, one leucine zipper domain, and onepotential glycosaminoglycan attachment site sequence.

[0438] One or more LRR domains are present in a variety of proteinsinvolved in protein-protein interactions. Such proteins include, forexample, proteins involved in signal transduction, cell-to-celladhesion, cell-to-extracellular matrix adhesion, cell development, DNArepair, RNA processing, and cellular molecular recognition processes.Specialized LRR domains, designated LRR amino terminal (LRRNT) domainsoften occur near the amino ends of a series of LRR domains. TANGO 366protein has nine LRR domains, arranged in two groups, the first groupincluding (from the amino terminus toward the carboxyl terminus of TANGO366) the LRRNT domain and four LRR domains, and the second groupincluding four LRR domains.

[0439] TANGO 366 is involved in one or more physiological processes inwhich these other LRR domain-containing proteins are involved, namelybinding of cells with extracellular proteins such as solubleextracellular proteins and cell surface proteins of other cells.

[0440] TANGO 366 comprises a leucine zipper region at about amino acidresidue 284 to about amino acid residue 305 (i.e., 284LdlsgtnLvplpeaLllhlpaL 305; SEQ ID NO: 458). Leucine zipper regions areknown to be involved in dimerization of proteins. Leucine zipper regionsinteract with one another, leading to formation of homo- orhetero-dimers between proteins, depending on their identity. Dimers ofproteins having leucine zipper regions can also interact with DNA. Thepresence in TANGO 366 of a leucine zipper region is a further indicationthat this protein is involved in protein-protein interactions.

[0441] The signal peptide prediction program SIGNALP (Nielsen et al.(1997) Protein Engineering 10:1-6) predicted that human TANGO 366protein includes an approximately 16 amino acid signal peptide (aminoacid residues 1 to about 16 of SEQ ID NO: 193; SEQ ID NO: 194) precedingthe mature TANGO 366 protein (amino acid residues 17 to 353 of SEQ IDNO: 193; SEQ ID NO: 195). Human TANGO 366 protein includes anextracellular domain (amino acid residues 17 to 216 of SEQ ID NO: 193;SEQ ID NO: 196), a transmembrane domain (amino acid residues 217 to 239of SEQ ID NO: 193; SEQ ID NO: 197), and a cytoplasmic domain (amino acidresidues 240 to 353 of SEQ ID NO: 193; SEQ ID NO: 198).

[0442]FIG. 16E depicts a hydrophobicity plot of human TANGO 366 protein.Relatively hydrophobic regions are above the dashed horizontal line, andrelatively hydrophilic regions are below the dashed horizontal line. Thehydrophobic region which corresponds to amino acid residues 1 to about16 of SEQ ID NO: 193 is the signal sequence of human TANGO 366 (SEQ IDNO: 194), and the hydrophobic region which corresponds to amino acidresidues 217 to 239 of SEQ ID NO: 193 is the transmembrane region ofTANGO 366 (SEQ ID NO: 197). As described elsewhere herein, relativelyhydrophilic regions are generally located at or near the surface of aprotein, and are more frequently effective immunogenic epitopes than arerelatively hydrophobic regions. For example, the region of human TANGO366 protein from about amino acid residue 315 to about amino acidresidue 330 appears to be located at or near the surface of the protein,while the region from about amino acid residue 290 to about amino acidresidue 305 appears not to be located at or near the surface.

[0443] The predicted molecular weight of human TANGO 366 protein withoutmodification and prior to cleavage of the signal sequence is about 37.8kilodaltons. The predicted molecular weight of the mature human TANGO366 protein without modification and after cleavage of the signalsequence is about 36.1 kilodaltons.

[0444] TANGO 366 exhibits limited sequence similarity to numerous cellsurface proteins, including proteins which serve as cell surfaceantigens, proteoglycans, and protein receptors. TANGO 366 protein, cDNA,and ORF exhibit sequence homology to the sequences corresponding to aGENBANK™ record having Accession No. HSM800846. The nucleotide sequenceof the DNA molecule described in GENBANK™ Accession No. HSM800846 isidentical to nucleotide residues 418 to 2628 of SEQ ID NO: 191. The cDNAof GENBANK™ Accession No. HSM800846 was obtained from uterine tissue,indicating that TANGO 366 is expressed in uterine tissue and thusinvolved in normal and aberrant physiological processes in uterinetissue. In addition, nucleotide residues 36 to 319 of the reversecomplement of SEQ ID NO: 191 exhibits significant homology withexpressed sequence tag (EST) 01904, which is disclosed in aninternational patent application having PCT Publication No. W093/16178.The ESTs described in that application were isolated from human braintissue. This is an indication that TANGO 366 is expressed in braintissue and thus is involved in normal and aberrant physiologicalprocesses in brain tissue.

[0445] Uses of TANGO 366 Nucleic Acids,

[0446] Polypeptides, and Modulators Thereof

[0447] TANGO 366 proteins are involved in disorders which affect bothtissues in which they are normally expressed and tissues in which theyare normally not expressed. Based on the observations that cDNAcorresponding to TANGO 366 occurs in a human normal prostate fibroblast,brain, and uterus cDNA libraries, it is evident that TANGO 366 proteinis involved in one or more biological processes which occur in prostate,brain, uterus, and other solid tissues. In particular, TANGO 366 isinvolved in modulating one or more of growth, proliferation, survival,differentiation, activity, morphology, and movement/migration of cellsof prostate, brain, uterus, and other solid tissues. Thus, TANGO 366 hasa role in disorders which affect the prostate, brain, uterus, and othersolid tissues and one or more of growth, proliferation, survival,differentiation, activity, morphology, and movement/migration of cellsin those tissues, as well as the biological function of organs (e.g.,the prostate) comprising such tissues.

[0448] Disorders which affect the prostate include the prostatedisorders described elsewhere in this disclosure. TANGO 366 proteins,nucleic acids encoding them, and agents that modulate activity orexpression of either of these can be used to prognosticate, diagnose,treat, and inhibit one or more of these disorders.

[0449] Examples of brain disorders include the brain disorders describedelsewhere in this disclosure. TANGO 366 proteins, nucleic acids encodingthem, and agents that modulate activity or expression of either of thesecan be used to prognosticate, diagnose, treat, and inhibit one or moreof these disorders.

[0450] Disorders which involve uterus tissue include the uterinedisorders described elsewhere in this disclosure. TANGO 366 proteins,nucleic acids encoding them, and agents that modulate activity orexpression of either of these can be used to prognosticate, diagnose,treat, and inhibit one or more of these disorders.

[0451] There are several indications that TANGO 366 is a cell surfaceprotein which is involved in binding a protein to the cell whichexpresses TANGO 366. For instance, presence in TANGO 366 of an aminoterminal extracellular domain that includes an LRRNT and four LRRdomains exemplifies the cell-surface protein interaction capability ofTANGO 366. In addition, the amino acid sequence similarity which TANGO366 exhibits with respect to several other cell surface protein-bindingproteins reinforces this view. TANGO 366 is involved in binding ananimal cell which expresses it with one or more of an extracellularfluid protein, a protein component of the extracellular matrix, asurface protein another cell of the same animal, and a surface proteinof a bacterium, fungus, or virus. Thus, TANGO 366 is involved inmodulating cell-to-cell adhesion, tissue and extracellular matrixinvasivity of cells, infectivity of cells by pathogens (e.g., bacteriaand viruses), endocrine signaling processes, tissue developmental andorganizational processes, and the like. TANGO 366 is involved indisorders in which these physiological processes are relevant. Suchdisorders include, for example, loss of control of cell growth, tumormetastasis, malformation of neurological connections, inflammation,immune and autoimmune responses, bacterial, fungal, and viralinfections, and the like. TANGO 366 proteins, nucleic acids encodingthem, and agents that modulate activity or expression of either of thesecan be used to prognosticate, diagnose, treat, and inhibit one or moreof these disorders.

[0452] INTERCEPT 394

[0453] A cDNA clone (designated jthKa041 fo2) encoding at least aportion of human INTERCEPT 394 protein was isolated from a human fetalkidney cDNA library. Human INTERCEPT 394 protein is predicted bystructural analysis to be a transmembrane protein.

[0454] The full length of the cDNA encoding human INTERCEPT 394 protein(FIG. 17; SEQ ID NO: 201) is 3743 nucleotide residues. The ORF of thiscDNA, nucleotide residues 320 to 2653 of SEQ ID NO: 201 (i.e., SEQ IDNO: 202), encodes a 778-amino acid residue protein (FIG. 17; SEQ ID NO:203), corresponding to a 778-residue transmembrane protein. It isrecognized that, in an alternative form, transcription of INTERCEPT 394protein can be initiated at the ATG codon located at nucleotide residues120-122 of SEQ ID NO 201. In this alternative form, INTERCEPT 394protein has, at the amino-terminal end of SEQ ID NO: 203, an additional61 amino acid residues, this additional portion having the amino acidsequence encoded by nucleotide residues 120-319 of SEQ ID NO: 201. Thesequences corresponding to the cDNA (SEQ ID NO: 217), ORF (SEQ ID NO:215), and protein (SEQ ID NO: 216) of this alternate form are listed inFIGS. 17H through 17M. In the following discussion, molecules of the twoforms of INTERCEPT 394 are referred to individually and collectively asmolecules of the corresponding type (e.g., cDNA or protein).

[0455] The invention thus includes purified human INTERCEPT 394 protein,both in the form of the immature 778 amino acid residue protein (SEQ IDNO: 203) and in the form of the mature 753 amino acid residue protein(SEQ ID NO: 205). Mature human INTERCEPT 394 proteins can be synthesizedwithout the signal sequence polypeptide at the amino terminus thereof,or it can be synthesized by generating immature INTERCEPT 394 proteinand cleaving the signal sequence therefrom.

[0456] The invention includes nucleic acid molecules which encode apolypeptide of the invention. Such nucleic acids include, for example, aDNA molecule having the nucleotide sequence listed in SEQ ID NO: 201 orsome portion thereof, such as the portion which encodes mature humanINTERCEPT 394 protein, immature human INTERCEPT 394 protein, or a domainof human INTERCEPT 394 protein. These nucleic acids are collectivelyreferred to as nucleic acids of the invention.

[0457] INTERCEPT 394 proteins and nucleic acid molecules encoding themcomprise a family of molecules having certain conserved structural andfunctional features.

[0458] A common domain present in INTERCEPT 394 proteins is a signalsequence.

[0459] In one embodiment, a INTERCEPT 394 protein contains a signalsequence corresponding to the portion of the protein from amino acidresidue 1 to about amino acid residue 25 of SEQ ID NO: 203 (SEQ ID NO:204). It is recognized that the carboxyl terminal boundary of the signalsequence can be located one or two residues from the residue identifiedabove (i.e., at residue 23, 24, 25, 26, or 27 of SEQ ID NO: 203). Thesignal sequence is cleaved during processing of the mature protein.

[0460] INTERCEPT 394 proteins can include an extracellular domain. HumanINTERCEPT 394 protein extracellular domains are located at about aminoacid residues 88 to 228 and 337 to 345 of SEQ ID NO: 203 (i.e., theextracellular domains having the sequences SEQ ID NOs: 208 and 212,respectively).

[0461] In addition, INTERCEPT 394 can include a transmembrane domain. Inone embodiment, a INTERCEPT 394 protein of the invention containstransmembrane domains corresponding to about amino acid residues 71 to87, 229 to 253, 320 to 336, and 346 to 364 of SEQ ID NO: 203 (i.e., thetransmembrane domains having the sequences SEQ ID NOs: 207, 209, 211,and 213, respectively).

[0462] The present invention includes INTERCEPT 394 proteins having acytoplasmic domain. The INTERCEPT 394 cytoplasmic domains are locatedfrom about amino acid residue 26 to 70, 254 to 319, and 365 to 778 ofSEQ ID NO: 203 (i.e., the cytoplasmic domains having the sequences SEQID NOs: 206, 210, and 214, respectively).

[0463] In an alternative form, INTERCEPT 394 proteins have cytoplasmicdomains located at about amino acid residues 88 to 228 and 337 to 345 ofSEQ ID NO: 203 (i.e., the cytoplasmic domains having the sequences SEQID NOs: 208 and 212, respectively); transmembrane domains correspondingto about amino acid residues 71 to 87, 229 to 253, 320 to 336, and 346to 364 of SEQ ID NO: 203 (i.e., the transmembrane domains having thesequences SEQ ID NOs: 207, 209, 211, and 213, respectively); andextracellular domains located from about amino acid residue 26 to 70,254 to 319, and 365 to 778 of SEQ ID NO: 203 (i.e., the extracellulardomains having the sequences SEQ ID NOs: 206, 210, and 214,respectively).

[0464] INTERCEPT 394 proteins typically comprise a variety of potentialpost-translational modification sites (often within an extracellulardomain), such as those described herein in Table XIII, as predicted bycomputerized sequence analysis of INTERCEPT 394 proteins using aminoacid sequence comparison software (comparing the amino acid sequence ofINTERCEPT 394 with the information in the PROSITE database {rel. 12.2;February 1995} and the Hidden Markov Models database {Rel. PFAM 3.3}).TABLE XIII Amino Acid Type of Potential Modification Site Residues ofAmino Acid or Domain SEQ ID NO: 203 Sequence N-glycosylation site  38 to41 NHSL  68 to 71 NGSL 163 to 166 NKSL 446 to 449 NFTVcAMP-/cGMP-dependent protein 671 to 674 RRES kinase phosphorylation siteProtein kinase C phosphorylation site  62 to 64 SAR 129 to 131 TQK 207to 209 SLK 226 to 228 SNR 568 to 570 SCR 604 to 606 TGR Casein kinase IIphosphorylation site  24 to 27 SCVD  50 to 53 TLPD 118 to 121 TWQE 129to 132 TQKE 143 to 146 TELD 254 to 257 SYAE 334 to 337 TIYD 400 to 403TRDE 552 to 555 SESE 614 to 617 SGVD 626 to 629 SVWE 680 to 683 SAPD 767to 770 SEDE Tyrosine kinase phosphorylation site 140 to 148 RELTELDIYN-myristoylation site  69 to 74 GSLITI 175 to 180 GLGEAV 185 to 190GLKYNF 264 to 269 GALGAR 319 to 324 GAFFAG 354 to 359 GVTVTV 453 to 458GVGDTC 477 to 482 GQTEAS 527 to 532 GAAASL 600 to 605 GQAPTG 630 to 635GQLQSL 685 to 690 GGEGAR 709 to 714 GAPETT 752 to 757 GQSASR

[0465] In various embodiments, the protein of the invention has at least1, 2, 4, 6, 10, 15, or 20 or more of the post-translational modificationsites described herein in Table XIII.

[0466] The signal peptide prediction program SIGNALP (Nielsen et al.(1997) Protein Engineering 10:1-6) predicted that human INTERCEPT 394protein includes an approximately 25 amino acid signal peptide (aminoacid residues 1 to about 25 of SEQ ID NO: 203; SEQ ID NO: 204) precedingthe mature INTERCEPT 394 protein (amino acid residues 26 to 778 of SEQID NO: 203; SEQ ID NO: 205). Human INTERCEPT 394 protein includes twoextracellular domains (amino acid residues 88 to 228 and 337 to 345 ofSEQ ID NO: 203; SEQ ID NOs: 208 and 212, respectively), fourtransmembrane domains (amino acid residues 71 to 87, 229 to 253, 320 to336, and 346 to 364 of SEQ ID NO: 203; SEQ ID NOs: 207, 209, 211, and213, respectively), and three cytoplasmic domains (amino acid residues26 to 70, 254 to 319, and 365 to 778 of SEQ ID NO: 203; SEQ ID NOs: 206,210, and 214, respectively).

[0467]FIG. 17G depicts a hydrophobicity plot of human INTERCEPT 394protein.

[0468] Relatively hydrophobic regions are above the dashed horizontalline, and relatively hydrophilic regions are below the dashed horizontalline. The hydrophobic region which corresponds to amino acid residues 1to about 25 of SEQ ID NO: 203 is the signal sequence of human INTERCEPT394 (SEQ ID NO: 204). Hydrophobic regions which corresponding to aminoacid residues 71 to 87, 229 to 253, 320 to 336, and 346 to 364 of SEQ IDNO: 203 are the transmembrane regions of INTERCEPT 394 (SEQ ID NOs: 207,209, 211, and 213, respectively). As described elsewhere herein,relatively hydrophilic regions are generally located at or near thesurface of a protein, and are more frequently effective immunogenicepitopes than are relatively hydrophobic regions. For example, theregion of human INTERCEPT 394 protein from about amino acid residue 205to about amino acid residue 225 appears to be located at or near thesurface of the protein, while the region from about amino acid residue410 to about amino acid residue 340 appears not to be located at or nearthe surface.

[0469] The predicted molecular weight of human INTERCEPT 394 proteinwithout modification and prior to cleavage of the signal sequence isabout 87.4 kilodaltons. The predicted molecular weight of the maturehuman INTERCEPT 394 protein without modification and after cleavage ofthe signal sequence is about 84.5 kilodaltons. Nucleotide residues 2944to 3482 of the reverse complement of SEQ ID NO: 201 exhibits significanthomology with EST clone BJ38, which is disclosed in an internationalpatent application having PCT Publication No. W098/45435. The ESTsdescribed in that application were isolated from human tissues. This isan indication that INTERCEPT 394 is expressed in the same tissues asthis EST clone and thus is involved in normal and aberrant physiologicalprocesses in these tissues.

[0470] Uses of INTERCEPT 394 Nucleic Acids,

[0471] Polypeptides, and Modulators Thereof

[0472] INTERCEPT 394 proteins are involved in disorders which affectboth tissues in which they are normally expressed and tissues in whichthey are normally not expressed. Based on the observations that cDNAcorresponding to INTERCEPT 394 occurs in a human fetal kidney cDNAlibrary, it is evident that INTERCEPT 394 protein is involved in one ormore biological processes which occur in kidney and other fetal andadult human tissues. In particular, INTERCEPT 394 is involved inmodulating one or more of growth, proliferation, survival,differentiation, activity, morphology, and movement/migration of cellsof kidney and other tissues. Thus, INTERCEPT 394 has a role in disorderswhich affect kidney and other tissues and one or more of growth,proliferation, survival, differentiation, activity, morphology, andmovement/migration of cells in those tissues, as well as the biologicalfunction of organs (e.g., the kidneys) comprising such tissues. Examplesof kidney disorders are described elsewhere in this disclosure.

[0473] The relatively large size of the carboxyl-terminal cytoplasmicdomain of INTERCEPT 394 is an indication that INTERCEPT 394 protein isinvolved in modulation of one or more intracellular processes. Thepresence of extracellular domains indicates that the activity ofINTERCEPT 394 can be modulated by binding thereto of ligands (i.e.,either naturally-occurring ligands or non-naturally-occurring ligandssuch as pharmaceutical agents). Because INTERCEPT 394 protein is anintegral membrane protein, it is capable of exerting its physiologicaleffect either by itself or in combination with one or more othermembrane proteins. INTERCEPT 394 is thus involved in either or both ofgeneration of signals which can be transmitted either to another protein(or other molecule) on the same side of the membrane or to a protein (orother molecule) on the opposite side of the membrane the membrane.INTERCEPT 394 can transmit such signals by binding a ligand, whereby itsconformation is altered such that the ability of INTERCEPT 394 tointeract with another molecule (e.g., to catalyze a reaction involvingthe molecule or by binding with the molecule) is altered upon bindingthe ligand. Alternatively, INTERCEPT 394 can be altered by beingpost-translationally modified (e.g., phosphorylated, glycosylated, ormyristoylated) such that the ability of INTERCEPT 394 to interact withanother molecule is altered upon post-translational modification.

[0474] Involvement of INTERCEPT 394 in one or more signal transmissionpathways is an indication that INTERCEPT 394 is involved inphysiological pathways involving such transmission. Thus, INTERCEPT 394is also involved in disorders which involve these signal transmissionpathways. Examples of physiological pathways that involve signaltransmission include cell nutrition and metabolism, cell proliferation,cell differentiation, apoptosis, chemotactic and chemokineticactivities, cell aggregation and attachment, cell movement, immunestimulation, hematopoiesis, metastasis, and the like. INTERCEPT 394 isthus involved in disorders relating to aberrant activity of one or moreof these signal transmission pathways. Such disorders include, forexample, carcinogenesis, tumor growth, tumor metastasis, angiogenesis,apoptosis, inappropriate blood coagulation (e.g., that involved inatherosclerosis, arteriosclerosis, and stroke), immune hypo- andhyper-stimulation, cell metabolism disorders (e.g., diabetes), endocrinedisorders (e.g., hypo- and hyper-thyroidism), mineral import and exportdisorders (e.g., osteoporosis, kidney stone formation, andhemochromatosis), and the like.

[0475] Presence of INTERCEPT 394 in the membrane of cells in which it isexpressed indicates that INTERCEPT 394 can be used as a diagnostictarget for detection or imaging of such cells. Furthermore, a portion ofINTERCEPT 394 (e.g., an extracellular domain) can be used to interferewith binding of a virus which normally binds with INTERCEPT 394, therebyinhibiting, reducing, or eliminating pathological effects associatedwith infection of a human by the virus.

[0476] INTERCEPT 400

[0477] A cDNA clone (designated jthkf014a09) encoding at least a portionof human INTERCEPT 400 protein was isolated from a human normalembryonic keratinocyte cDNA library. A corresponding murine cDNA clone(designated jtmba232b12) was isolated from a brain polysome cDNAlibrary. Human and murine INTERCEPT 400 proteins are predicted bystructural analysis to be transmembrane proteins.

[0478] The full length of the cDNA encoding human INTERCEPT 400 protein(FIG. 18; SEQ ID NO: 221) is 2989 nucleotide residues. The open readingframe (ORF) of this cDNA, nucleotide residues 206 to 1000 of SEQ ID NO:221 (i.e., SEQ ID NO: 222), encodes a 265-amino acid residue immatureprotein (FIG. 18; SEQ ID NO: 223), corresponding to a 219-residuetransmembrane protein.

[0479] The invention thus includes purified human INTERCEPT 400 protein,both in the form of the immature 265 amino acid residue protein (SEQ IDNO: 223) and in the form of the mature 219 amino acid residue protein(SEQ ID NO: 225). The invention also includes purified murine INTERCEPT400 protein, which is a 180-amino acid residue transmembrane protein(SEQ ID NO: 243). Mature human INTERCEPT 400 proteins can be synthesizedwithout the signal sequence polypeptide at the amino terminus thereof,or it can be synthesized by generating immature INTERCEPT 400 proteinand cleaving the signal sequence therefrom.

[0480] The invention includes nucleic acid molecules which encode apolypeptide of the invention. Such nucleic acids include, for example, aDNA molecule having the nucleotide sequence listed in SEQ ID NO: 221 orsome portion thereof or SEQ ID NO: 241 or some portion thereof, such asthe portion which encodes mature human or murine INTERCEPT 400 protein,immature human INTERCEPT 400 protein, or a domain of human or murineINTERCEPT 400 protein. These nucleic acids are collectively referred toas nucleic acids of the invention.

[0481] INTERCEPT 400 proteins and nucleic acid molecules encoding themcomprise a family of molecules having certain conserved structural andfunctional features.

[0482] A common domain present in INTERCEPT 400 proteins is a signalsequence. In one embodiment, a INTERCEPT 400 protein contains a signalsequence corresponding to the portion of the protein from amino acidresidue 1 to about amino acid residue 46 of SEQ ID NO: 223 (SEQ ID NO:224). It is recognized that the carboxyl terminal boundary of the signalsequence can be located one or two residues from the residue identifiedabove (i.e., at residue 44, 45, 46, 47, or 48 of SEQ ID NO: 223). Thesignal sequence is cleaved during processing of the mature protein.

[0483] INTERCEPT 400 proteins can also include an extracellular domain.Human INTERCEPT 400 protein includes extracellular domains located fromabout amino acid residues 47 to 62, 154 to 164, and 218 to 231 of SEQ IDNO: 223 (i.e., the extracellular domains having the amino acid sequencesSEQ ID NOs: 226, 230, and 234, respectively). Murine INTERCEPT 400protein includes extracellular domains located from about amino acidresidues 61 to 71 and 125 to 140 of SEQ ID NO: 243 (i.e., theseextracellular domains having the amino acid sequences SEQ ID NOs: 246and 250, respectively).

[0484] In addition, INTERCEPT 400 can include a transmembrane domain.Human INTERCEPT 400 protein includes transmembrane domains correspondingto about amino acid residues 63 to 79, 137 to 153, 165 to 183, 194 to217, and 232 to 251 of SEQ ID NO: 223 (i.e., the transmembrane domainshaving the sequences SEQ ID NOs: 227, 229, 231, 233, and 235,respectively). Murine INTERCEPT 400 protein includes transmembranedomains corresponding to about amino acid residues 44 to 60, 72 to 90,101 to 124, and 141 to 160 of SEQ ID NO: 243 (i.e., the transmembranedomains having the sequences SEQ ID NOs: 245, 247, 249, and 251,respectively).

[0485] The present invention includes INTERCEPT 400 proteins having acytoplasmic domain. Human INTERCEPT 400 cytoplasmic domains are locatedfrom about amino acid residue 80 to 136, 184 to 193, and 252 to 265 ofSEQ ID NO: 223 (i.e., the cytoplasmic domains having the sequences SEQID NOs: 228, 232, and 236, respectively). Murine INTERCEPT 400cytoplasmic domains are located from about amino acid residue 1 to 43,91 to 100, and 161 to 174 of SEQ ID NO: 243 (i.e., the cytoplasmicdomains having the sequences SEQ ID NOs: 244, 248, and 252,respectively).

[0486] It is recognized that, in one form, murine INTERCEPT 400 proteincan include an amino terminal portion approximately 60-120 (likely80-100) amino acid residues in length.

[0487] In an alternative embodiment, human INTERCEPT 400 proteins havecytoplasmic domains located from about amino acid residues 47 to 62, 154to 164, and 218 to 231 of SEQ ID NO: 223 (i.e., the cytoplasmic domainshaving the amino acid sequences SEQ ID NOs: 226, 230, and 234,respectively); transmembrane domains corresponding to about amino acidresidues 63 to 79, 137 to 153, 165 to 183, 194 to 217, and 232 to 251 ofSEQ ID NO: 223 (i.e., the transmembrane domains having the sequences SEQID NOs: 227, 229, 231, 233, and 235, respectively); and extracellulardomains are located from about amino acid residue 80 to 136, 184 to 193,and 252 to 265 of SEQ ID NO: 223 (i.e., the extracellular domains havingthe sequences SEQ ID NOs: 228, 232, and 236, respectively).

[0488] In an alternative embodiment, murine INTERCEPT 400 proteins havecytoplasmic domains located from about amino acid residues 61 to 71 and125 to 140 of SEQ ID NO: 243 (i.e., these cytoplasmic domains having theamino acid sequences SEQ ID NOs: 246 and 250, respectively);transmembrane domains corresponding to about amino acid residues 44 to60, 72 to 90, 101 to 124, and 141 to 160 of SEQ ID NO: 243 (i.e., thetransmembrane domains having the sequences SEQ ID NOs: 245, 247, 249,and 254, respectively); and extracellular domains are located from aboutamino acid residue 1 to 43, 91 to 100, and 161 to 174 of SEQ ID NO: 243(i.e., the extracellular domains having the sequences SEQ ID NOs: 244,248, and 255, respectively).

[0489] INTERCEPT 400 proteins typically comprise a variety of potentialpost-translational modification sites (often within an extracellulardomain), such as those described herein in Tables XIV (for humanINTERCEPT 400) and XV (for murine INTERCEPT 400), as predicted bycomputerized sequence analysis of INTERCEPT 400 proteins using aminoacid sequence comparison software (comparing the amino acid sequence ofINTERCEPT 400 with the information in the PROSITE database {rel. 12.2;February 1995} and the Hidden Markov Models database {Rel. PFAM 3.3}).TABLE XIV Amino Acid Type of Potential Modification Site Residues AminoAcid or Domain of SEQ ID NO: 223 Sequence N-glycosylation site  2 to 5NMSV cAMP-/cGMP-dependent protein 259 to 262 RKTT kinase phosphorylationsite Protein kinase C phosphorylation site 155 to 157 SYK 191 to 193 SRK261 to 263 TTK Casein kinase II phosphorylation site  7 to 10 TLQE  97to 100 SVCD 155 to 158 SYKD 262 to 265 TKAE N-myristoylation site  77 to82 GALRTG  93 to 98 GLKQSV 209 to 214 GCVVNY

[0490] TABLE XV Amino Acid Type of Potential Modification Site ResiduesAmino Acid or Domain of SEQ ID NO: 243 Sequence cAMP-/cGMP-dependentprotein 168 to 171 KKAT kinase phosphorylation site Protein kinase Cphosphorylation site  62 to 64 SYK  98 to 100 SRK Casein kinase IIphosphorylation site  4 to 7 SVCD  62 to 65 SYKD 171 to 174 TKAEN-myristoylation site 116 to 121 GCVINY

[0491] In various embodiments, the protein of the invention has at least1, 2, 4, 6, 10, 15, or 20 or more of the post-translational modificationsites described herein in Tables XIV and XV.

[0492] The signal peptide prediction program SIGNALP (Nielsen et al.(1997) Protein Engineering 10: 1-6) predicted that human INTERCEPT 400protein includes an approximately 46 amino acid signal peptide (aminoacid residues 1 to about 46 of SEQ ID NO: 223; SEQ ID NO: 224) precedingthe mature INTERCEPT 400 protein (amino acid residues 47 to 265 of SEQID NO: 223; SEQ ID NO: 225). Human INTERCEPT 400 protein includes threeextracellular domains (amino acid residues 47 to 62, 154 to 164, and 218to 231 of SEQ ID NO: 223; SEQ ID NOs: 226, 230, and 234, respectively),five transmembrane domains (amino acid residues 63 to 79, 137 to 153,165 to 183, 194 to 217, and 232 to 251 of SEQ ID NO: 223; SEQ ID NOs:227, 229, 231, 233, and 235, respectively), and three intracellulardomains (amino acid residues 80 to 136, 184 to 193, and 252 to 265 ofSEQ ID NO: 223; SEQ ID NOs: 228, 232, and 236, respectively).

[0493]FIG. 18D depicts a hydrophobicity plot of human INTERCEPT 400protein. Relatively hydrophobic regions are above the dashed horizontalline, and relatively hydrophilic regions are below the dashed horizontalline. The hydrophobic region which corresponds to amino acid residues 1to about 46 of SEQ ID NO: 223 is the signal sequence of human INTERCEPT400 (SEQ ID NO: 224). As described elsewhere herein, relativelyhydrophilic regions are generally located at or near the surface of aprotein, and are more frequently effective immunogenic epitopes than arerelatively hydrophobic regions. For example, the region of humanINTERCEPT 400 protein from about amino acid residue 218 to about aminoacid residue 231 appears to be located at or near the surface of theprotein, while the region from about amino acid residue 80 to aboutamino acid residue 95 appears not to be located at or near the surface.

[0494] The predicted molecular weight of human INTERCEPT 400 proteinwithout modification and prior to cleavage of the signal sequence isabout 31.4 kilodaltons.

[0495] The predicted molecular weight of the mature human INTERCEPT 400protein without modification and after cleavage of the signal sequenceis about 25.8 kilodaltons.

[0496] Human INTERCEPT 400 exhibits sequence similarity to murine Cig30protein (GENBANK™ Accession No. U97107), as indicated herein in FIG.18L, which lists an alignment (made using the ALIGN software; pam120.matscoring matrix; gap penalties −12/−4) of the amino acid sequences ofthese proteins. FIGS. 18M through 180 depict an alignment (also madeusing the ALIGN software; pam120.mat scoring matrix; gap penalties−12/−4) of the nucleotide sequences of the ORFs of human INTERCEPT 400(SEQ ID NO: 222) and Cig30 (SEQ ID NO: 238). In these alignments (madeusing the ALIGN software; pam120.mat scoring matrix, gap penalties−12/−4), the amino acid sequences of these two proteins are 43.3%identical and the ORF nucleotide sequences corresponding to these twoproteins are 56.8% identical. The cDNAs corresponding to these twoproteins were found to be 48.4% identical using the LALIGN software(pam120.mat scoring matrix; gap penalties −12/−4).

[0497] The length of the incomplete cDNA encoding the carboxyl-terminalportion of murine INTERCEPT 400 protein (FIG. 18; SEQ ID NO: 241) is2032 nucleotide residues. The ORF of this cDNA, nucleotide residues 3 to524 (SEQ ID NO: 242), encodes a protein comprising at least 180 aminoacid residues (FIG. 18; SEQ ID NO: 243). It is recognized that murineINTERCEPT 400 protein has about 60-120, more likely 80-100, additionalamino acid residues at the amino terminal end thereof.

[0498] The signal peptide prediction program SIGNALP (Nielsen et al.(1997) Protein Engineering 10:1-6) predicted that the portion of murineINTERCEPT 400 protein described herein includes at least twoextracellular domains (amino acid residues 61 to 71 and 125 to 140 ofSEQ ID NO: 243; SEQ ID NOs: 246 and 250, respectively), at least fourtransmembrane domains (amino acid residues 44 to 60, 72 to 90, 101 to124, and 141 to 160 of SEQ ID NO: 243; SEQ ID NOs: 245, 247, 249, and254, respectively), and at least three cytoplasmic domains (amino acidresidue 1 to 43, 91 to 100, and 161 to 174 of SEQ ID NO: 243; SEQ IDNOs: 244, 248, and 255, respectively).

[0499]FIG. 18G depicts a hydrophobicity plot of murine INTERCEPT 400protein.

[0500] Relatively hydrophobic regions are above the dashed horizontalline, and relatively hydrophilic regions are below the dashed horizontalline. Hydrophobic regions corresponds to the identified transmembraneregions of murine INTERCEPT 400. As described elsewhere herein,relatively hydrophilic regions are generally located at or near thesurface of a protein, and are more frequently effective immunogenicepitopes than are relatively hydrophobic regions. For example, theregion from about amino acid residue 125 to about amino acid residue 140appears to be located at or near the surface of the protein, while theregion from about amino acid residue 14 to about amino acid residue 19appears not to be located at or near the surface

[0501] The predicted molecular weight of the portion of murine INTERCEPT400 protein described herein is about 20.6 kilodaltons.

[0502] Human and murine INTERCEPT 400 proteins exhibit considerablesequence similarity, as indicated herein in FIGS. 18H through 18K. FIG.18H depicts an alignment of human and murine INTERCEPT 400 amino acidsequences (SEQ ID NOs: 223 and 243, respectively). In this alignment(made using the ALIGN software; pam120.mat scoring matrix; gap penalties−12/−4), the proteins are 94.8% identical in the overlapping region(i.e., 163 identical residues out of 172 residues in the overlappingregion, which includes amino acid residues 94-265 of SEQ ID NO: 223 andamino acid residues I-174 of SEQ ID NO: 243). The human and murine ORFsencoding INTERCEPT 400 are 92.8% identical in the overlapping portions(i.e., nucleotide residues 280-795 of SEQ ID NO: 222 and nucleotideresidues 1-522 of SEQ ID NO: 242), as assessed using the same softwareand parameters and as indicated in FIGS. 181 through 18K in an alignmentmade using the ALIGN software (pam120.mat scoring matrix; gap penalties−12/−4).

[0503] The partial nucleotide sequences of a rat cDNA clone (designatedjtmba232b12; SEQ ID NO: 251) and ORF (SEQ ID NO: 252) encoding INTERCEPT400 are depicted in FIGS. 18P and 18Q, together with the amino acidsequence (SEQ ID NO: 253) of the portion of the protein encoded by thesenucleic acids. An alignment (made using the ALIGN software; pam120.matscoring matrix; gap penalties −12/−4) of human, murine and rat INTERCEPT400 amino acid sequences is listed in FIG. 18R.

[0504] Uses of INTERCEPT 400 Nucleic Acids,

[0505] Polypeptides, and Modulators Thereof

[0506] INTERCEPT 400 proteins are involved in disorders which affectboth tissues in which they are normally expressed and tissues in whichthey are normally not expressed. Based on the observations that cDNAcorresponding to INTERCEPT 400 occurs in a human normal embryonickeratinocyte cDNA library and in a murine brain polysome cDNA library,it is evident that INTERCEPT 400 protein is involved in one or morebiological processes which occur in these tissues. In particular,INTERCEPT 400 is involved in modulating one or more of growth,proliferation, survival, differentiation, activity, morphology, andmovement/migration of cells of these tissues. INTERCEPT 400 is involvedin modulating the structure of extracellular matrix which contacts or isin fluid communication with cells of these tissues. Thus, INTERCEPT 400has a role in disorders which affect these cells and one or more oftheir growth, proliferation, survival, differentiation, activity,morphology, and movement/migration, as well as the biological functionof organs comprising one or more of these tissues.

[0507] Examples of brain disorders are described elsewhere in thisdisclosure. INTERCEPT 400 proteins, nucleic acids encoding them, andagents that modulate activity or expression of either of these can beused to prognosticate, diagnose, treat, and inhibit one or more of thesedisorders.

[0508] Examples of skin disorders with which INTERCEPT 400 can beassociated are described elsewhere in this disclosure. INTERCEPT 400proteins, nucleic acids encoding them, and agents that modulate activityor expression of either of these can be used to prognosticate, diagnose,treat, and inhibit one or more of these disorders.

[0509] Murine Cig30 protein, with which human INTERCEPT 400 sharessignificant amino acid sequence homology, is an integral membraneprotein that is involved in recruitment and thermogenesis in brownadipose tissue in mice (Tvrdik et al., 1997, J.

[0510] Biol. Chem. 272:31738-31746). Yeast proteins which sharesignificant homology with murine Cig30 and human, murine, and ratINTERCEPT 400 protein include proteins encoded by yeast genes SUR4(APAI) and FENI (GNSI). These proteins are involved in phospholipidmetabolism, sterol synthesis, budding, activation of glucose-regulatedgenes, glucose uptake, and glucan synthesis (Desfarges et al., 1993,Yeast 9:267-277; Silve et al., 1996, Mol. Cell. Biol. 16:2719-2727;Durrens et al., 1995, Curr. Genet. 27:213-216; Garcia-Arranz, 1994, J.Biol. Chem. 269:18076-18082; El-Sherbeini et al., 1995, J. Bacteriol.177:3227-3234). These activities relate to remodeling of the plasmamembrane and actin cytoskeleton in response to growth signals, mostlikely by modulating interaction between membrane phospholipids and thecytoskeleton. Thus, INTERCEPT 400 protein is involved in one or more ofthese activities, such as in immune stimulation, proliferation ofleukocytes, generation and prolongation of an immune response, controlof cellular metabolic processes, and the like.

[0511] INTERCEPT 400 is involved in generation, accumulation, andregulation of brown adipose tissue and other adipose tissues in humans,and is therefore involved in body temperature regulation, lipidmetabolism, carbohydrate metabolism, body weight regulation, and thelike. Thus, INTERCEPT 400 is implicated in disorders which relate toaberrance or imbalance in the normal physiological regulation of theseprocesses. INTERCEPT 400 is also involved in disorders which relate toaberrant proliferation and growth of cells. Examples of disorders inwhich INTERCEPT 400 is involved include obesity, unusual susceptibilityor insensitivity to heat or cold, diabetes, arteriosclerosis,atherosclerosis, cancer, hypo- and hyper-immune disorders (e.g.,acquired immune deficiency syndrome and auto-immune disorders), immuneproliferation, and the like. INTERCEPT 400 proteins, nucleic acidsencoding them, and agents that modulate activity or expression of eitherof these can be used to prognosticate, diagnose, treat, and inhibit oneor more of these disorders.

[0512] Chromosomal mapping data have been used to locate the geneencoding human INTERCEPT 400 at chromosome 4, between markers D4S1616and D4S1611 (115.8-119.6 centimorgans). A form of iris hypoplasiaassociated with early onset glaucoma has been linked with thischromosomal region. Human INTERCEPT 400 allelic variants can includeINTERCEPT 400 nucleotide sequence polymorphisms (e.g., nucleotidesequences that vary from SEQ ID NO: 221) that map to this chromosomalregion.

[0513] INTERCEPT 217

[0514] A cDNA clone (designated jthqc035f08) encoding at least a portionof human INTERCEPT 217 protein was isolated from a human prostate cDNAlibrary. The human INTERCEPT 217 protein is predicted by structuralanalysis to be a transmembrane protein. In addition, cDNA clones(including those designated jtmca047g07, jTmob373b05, and jambd078d12)encoding at least a portion of murine INTERCEPT 217 protein wereisolated from murine cDNA libraries.

[0515] The full length of the cDNA encoding human INTERCEPT 217 protein(FIG. 19; SEQ ID NO: 271) is 2895 nucleotide residues. The ORF of thiscDNA, nucleotide residues 215 to 1579 of SEQ ID NO: 271 (i.e., SEQ IDNO: 272), encodes a 455-amino acid transmembrane protein (FIG. 19; SEQID NO: 273). The murine ORF (FIG. 19; SEQ ID NO: 362) comprises at least962 nucleotide residues. The protein encoded by the murine ORF comprisesat least 320 amino acid residues (i.e., SEQ ID NO: 363), and is also atransmembrane protein.

[0516] The invention also includes purified human INTERCEPT 217 protein,both in the form of the immature 455 amino acid residue protein (SEQ IDNO: 273) and in the form of the mature, approximately 435 amino acidresidue protein (SEQ ID NO: 275). Mature human INTERCEPT 217 protein canbe synthesized without the signal sequence polypeptide at the aminoterminus thereof, or it can be synthesized by generating immatureINTERCEPT 217 protein and cleaving the signal sequence therefrom.

[0517] The invention thus includes purified murine INTERCEPT 217protein, both in the immature form comprising the 320 amino acidresidues of SEQ ID NO: 363 and in the mature form comprising theapproximately 305 carboxyl terminal amino acid residues of SEQ ID NO:363 (i.e., comprising SEQ ID NO: 365). Mature murine INTERCEPT 217protein can be synthesized without the signal sequence polypeptide atthe amino terminus thereof, or it can be synthesized by generatingimmature INTERCEPT 217 protein and cleaving the signal sequencetherefrom.

[0518] The invention includes nucleic acid molecules which encode anINTERCEPT 217 polypeptide of the invention. Such nucleic acids include,for example, a DNA molecule having the nucleotide sequence listed in SEQID NO: 271, in SEQ ID NO: 362 (i.e., the murine ORF), or in some portionof either of these, such as the portion which encodes mature humanINTERCEPT 217 protein, immature human INTERCEPT 217 protein, or a domainof human INTERCEPT 217 protein. These nucleic acids are collectivelyreferred to as INTERCEPT 217 nucleic acids of the invention.

[0519] INTERCEPT 217 proteins and nucleic acid molecules encoding themcomprise a family of molecules having certain conserved structural andfunctional features. Each of these molecules is included in theinvention.

[0520] A common domain present in INTERCEPT 217 proteins is a signalsequence. In one embodiment, a INTERCEPT 217 protein contains a signalsequence corresponding to about amino acid residues 1 to 20 of SEQ IDNO: 273 (SEQ ID NO: 274). The signal sequence is cleaved duringprocessing of the mature protein.

[0521] INTERCEPT 217 proteins can include an extracellular domain. Thehuman INTERCEPT 217 protein extracellular domain is located from aboutamino acid residue 21 to about amino acid residue 383 of SEQ ID NO: 273(SEQ ID NO: 276). The murine INTERCEPT 217 protein extracellular domainis located from about amino acid residue 17 to about amino acid residue213 of SEQ ID NO: 363 (SEQ ID NO: 366).

[0522] In addition, INTERCEPT 217 includes a transmembrane domain. Asused herein, a “transmembrane domain” refers to an amino acid sequencewhich is at least about 20 to 25 amino acid residues in length and whichcontains at least about 65-70% hydrophobic amino acid residues such asalanine, leucine, phenylalanine, protein, tyrosine, tryptophan, orvaline. In a preferred embodiment, a transmembrane domain contains atleast about 15 to 30 amino acid residues, preferably about 20-25 aminoacid residues, and has at least about 60-80%, more preferably 65-75%,and more preferably at least about 70% hydrophobic residues. Thus, inone embodiment, an INTERCEPT 217 protein of the invention contains atransmembrane domain corresponding to about amino acid residues 384 to403 of SEQ ID NO: 273 (SEQ ID NO: 277) or to about amino acid residues214 to 233 of SEQ ID NO: 363 (SEQ ID NO: 367).

[0523] The present invention includes INTERCEPT 217 proteins having acytoplasmic domain, particularly including proteins having acarboxyl-terminal cytoplasmic domain. The human INTERCEPT 217cytoplasmic domain is located from about amino acid residue 404 to aminoacid residue 455 of SEQ ID NO: 273 (SEQ ID NO: 278). The murineINTERCEPT 217 cytoplasmic domain is located from about amino acidresidue 234 to amino acid residue 320 of SEQ ID NO: 363 (SEQ ID NO:368).

[0524] In one embodiment, the amino acid residues of human INTERCEPT 217corresponding to SEQ ID NO: 278 are part of an extracellular domain, andthe amino acid residues corresponding to SEQ ID NO: 276 are part of acytoplasmic domain. In another embodiment, the amino acid residues ofmurine INTERCEPT 217 corresponding to SEQ ID NO: 368 are part of anextracellular domain, and the amino acid residues corresponding to SEQID NO: 366 are part of a cytoplasmic domain.

[0525] INTERCEPT 217 proteins typically comprise a variety of potentialpost-translational modification sites (often within an extracellulardomain), such as those described herein in Tables XVIA (for humanINTERCEPT 217) and XVIB (for murine INTERCEPT 217), as predicted bycomputerized sequence analysis of INTERCEPT 217 proteins using aminoacid sequence comparison software (comparing the amino acid sequence ofINTERCEPT 217 with the information in the PROSITE database {rel. 12.2;February 1995} and the Hidden Markov Models database {Rel. PFAM 3.3}).In certain embodiments, a protein of the invention has at least 1, 2, 4,6, or 10 or more of the post-translational modification sites listed inTables XVIA and XVIB. TABLE XVIA Amino Acid Type of PotentialModification Site Residues Amino Acid or Domain of SEQ ID NO: 273Sequence N-glycosylation site 107 to 110 NASG 272 to 275 NCSS 301 to 304NTSV 362 to 365 NQTH 368 to 371 NVSV Protein kinase C phosphorylationsite 120 to 122 TLR 192 to 194 SNR 295 to 297 SLR Casein kinase IIphosphorylation site 199 to 202 SVPE 440 to 443 TPPD Tyrosine KinasePhosphorylation Site 282 to 289 KRPEEHLY N-myristoylation site  8 to 13GTLLCM  19 to 24 GTPDSE 103 to 108 GVFVNA 179 to 184 GLSATH 323 to 328GSRDGS 348 to 353 GLFVCL 390 to 395 GCAVGL 449 to 454 GQASTS Leucinezipper pattern  45 to 66 See FIG. 19 Leucine rich repeat amino terminal 33 to 61 See FIG. 19 domain (LLRNT) Leucine rich repeat (LRR) Domain 62 to 85 See FIG. 19  86 to 109 See FIG. 19 110 to 133 See FIG. 19 134to 157 See FIG. 19 158 to 181 See FIG. 19 184 to 207 See FIG. 19 Leucinerich repeat carboxyl terminal 219 to 274 See FIG. 19 (LLRCT) domain

[0526] TABLE XVIB Amino Acid Type of Potential Modification SiteResidues Amino Acid or Domain of SEQ ID NO: 363 Sequence N-glycosylationsite 102 to 105 NCSV 131 to 134 NTSV 192 to 195 NQTL 198 to 201 NVSVcAMP-and cGMP-dependent protein 280 to 283 RKAS kinase site Proteinkinase C phosphorylation site 125 to 127 SLR 143 to 145 SPK 279 to 281SRK Casein kinase II phosphorylation site  29 to 32 SIPE 273 to 276 TPPDN-myristoylation site  9 to 14 GLGLTR 178 to 183 GVFVCL 220 to 225GCIVGL 239 to 244 GCCHCC Amidation Site 293 to 296 PGKK ImmunoglobulinDomain  14 to 37 See FIG. 19 Leucine rich repeat (LRR) Domain  49 to 104See FIG. 19 Leucine rich repeat carboxyl terminal 123 to 184 See FIG. 19(LLRCT) domain

[0527] Among the domains that occur in INTERCEPT 217 proteins are LRRdomains, LRRNT domains, LRRCT domains, and immunoglobulin domains. Inone embodiment, the protein of the invention has at least one domainthat is at least 55%, preferably at least about 65%, more preferably atleast about 75%, yet more preferably at least about 85%, and mostpreferably at least about 95% identical to one of these domains. Inother embodiments, the protein has at least one of each of the LRR,LRRNT, and LRRCT domains described herein in Tables XVIA and XVIB. Inother embodiments, the protein has at least one LRRNT domain, at leastone LRRCT domain, and a plurality of (e.g., 2, 3, 4, or more) LRRdomains.

[0528] One or more LRR domains are present in a variety of proteinsinvolved in protein-protein interactions. Such proteins include, forexample, proteins involved in signal transduction, cell-to-celladhesion, cell-to-extracellular matrix adhesion, cell development, DNArepair, RNA processing, and cellular molecular recognition processes.Specialized LRR domains, designated LRR amino terminal (LRRNT) domainsand LRR carboxyl terminal (LRRCT) domains often occur near the amino andcarboxyl, respectively, ends of a series of LRR domains. Human INTERCEPT217 protein has eight clustered LRR domains, including (from the aminoterminus toward the carboxyl terminus of INTERCEPT 217) an LRRNT domain,six LRR domains, and an LRRCT domain.

[0529] The organization of LRR domains in human INTERCEPT 217 proteinclosely mirrors the organization of LRR domains in human plateletglycoprotein IB alpha chain precursor (GP-IBa), which also has eightclustered LRR domains from about amino acid residue 19 to about aminoacid residue 281 thereof. The eight LRR domains of GP-IBa include anLRRNT domain at the end of the cluster nearest the amino terminus ofGP-IBA and an LRRCT domain at the end of the cluster nearest thecarboxyl terminus of GP-IBA. GP-IBa is a membrane-bound protein of humanplatelets that is involved in binding of von Willebrand's factor and inaggregation of platelets during thrombus formation. Thus, INTERCEPT 217is involved in both normal and aberrant physiological activitiesinvolving blood clotting and thrombus formation. Examples of disordersinvolving such activities include, for example, stroke, embolism (e.g.,cerebral, renal, and pulmonary emboli), hemophilia, restenotic injury,prosthesis-associated thrombogenesis, atherosclerosis, andarteriosclerosis.

[0530] INTERCEPT 217 is involved in one or more physiological processesin which these other LRR domain-containing proteins are involved, namelybinding of cells with extracellular proteins such as solubleextracellular proteins and cell surface proteins of other cells.

[0531] Human INTERCEPT 217 comprises a leucine zipper region at aboutamino acid residue 45 to about amino acid residue 66 (i.e., 45LsctglgLqdvpaeLpaa tadL 66; SEQ ID NO: 459). Leucine zipper regions areknown to be involved in dimerization of proteins. Leucine zipper regionsinteract with one another, leading to formation of homo- orhetero-dimers between proteins, depending on their identity. Thepresence in INTERCEPT 217 of a leucine zipper region is a furtherindication that this protein is involved in protein-proteininteractions.

[0532] The amino acid sequence of human INTERCEPT 217 protein includesmultiple potential proline-rich Src homology 3 (SH3) domain bindingsites in the cytoplasmic portion of the protein. SH3 domains mediatespecific assembly of protein complexes, presumably by interacting withproline-rich protein domains (Morton and Campbell (1994) Curr. Biol.4:615-617). SH3 domains also mediate interactions between proteinsinvolved in transmembrane signal transduction. Coupling of proteinsmediated by SH3 domains has been implicated in a variety ofphysiological systems, including those involving regulation of cellgrowth and proliferation, endocytosis, and activation of respiratoryburst.

[0533] SH3 domains have been described in the art (e.g., Mayer et al.(1988) Nature 332:272-275; Musacchio et al. (1992) FEBS Lett. 307:55-61;Pawson and Schlessinger (1993) Curr. Biol. 3:434-442; Mayer andBaltimore (1993) Trends Cell Biol. 3:8-13; Pawson (1993) Nature373:573-580), and occur in a variety of cytoplasmic proteins, includingseveral (e.g., protein tyrosine kinases) involved in transmembranesignal transduction. Among the proteins in which one or more SH3 domainsoccur are protein tyrosine kinases such as those of the Src, Abl, Bkt,Csk and ZAP70 families, mammalian phosphatidylinositol-specificphospholipases C-gamma-1 and -2, mammalian phosphatidylinositol 3-kinaseregulatory p85 subunit, mammalian Ras GTPase-activating protein (GAP),proteins which mediate binding of guanine nucleotide exchange factorsand growth factor receptors (e.g., vertebrate GRB2, Caenorhabditiselegans sem-5, and Drosophila DRK proteins), mammalian Vav oncoprotein,guanidine nucleotide releasing factors of the CDC 25 family (e.g., yeastCDC25, yeast SCD25, and fission yeast ste6 proteins), MAGUK proteins(e.g., mammalian tight junction protein ZO-1, vertebrate erythrocytemembrane protein p55, C. elegans protein lin-2, rat protein CASK, andmammalian synaptic proteins SAP90/PSD-95, CHAPSYN-110/PSD-93, SAP97/DLG1, and SAP102), proteins which interact with vertebrate receptor proteintyrosine kinases (e.g., mammalian cytoplasmic protein Nck andoncoprotein Crk), chicken Src substrate p80/85 protein (cortactin),human hemopoietic lineage cell specific protein Hs 1, mammaliandihydrouridine-sensitive L-type calcium channel beta subunit, humanmyasthenic syndrome antigen B (MSYB), mammalian neutrophil cytosolicactivators of NADPH oxidase (e.g., p47 {NCF-1}, p67 {NCF-2}, and C.elegans protein B0303.7), myosin heavy chains (MY03) from amoebae, fromslime molds, and from yeast, vertebrate and Drosophila spectrin andfodrin alpha chain proteins, human amphiphysin, yeast actin-bindingproteins ABP 1 and SLA3, yeast protein BEM 1, fission yeast protein scd2(ra13), yeast BEM1-binding proteins B012 (BEB1) and BOB1 (BOI1), yeastfusion protein FUS1, yeast protein RSV167, yeast protein SSU8-, yeasthypothetical proteins YAR014c, YFR024c, YHL002w, YHR016c, YJL020C, andYHR114w, hypothetical fission yeast protein SpAC12C2.05c, and C. eleganshypothetical protein F42H10.3. Of these proteins, multiple SH3 domainsoccur in vertebrate GRB2 protein, C. elegans sem-5 protein, DrosophilaDRK protein, oncoprotein Crk, mammalian neutrophil cytosolic activatorsof NADPH oxidase p47 and p67, yeast protein BEMI, fission yeast proteinscd2, yeast hypothetical protein YHR114w, mammalian cytoplasmic proteinNck, C. elegans neutrophil cytosolic activator of NADPH oxidase B0303.7,and yeast actin-binding protein SLA1. Of these proteins, three or moreSH3 domains occur in mammalian cytoplasmic protein Nck, C. elegansneutrophil cytosolic activator of NADPH oxidase B0303.7, and yeastactin-binding protein SLA1. The presence of SH3 domain binding sites inINTERCEPT 217 indicates that INTERCEPT 217 interacts with one or more ofthese and other SH3 domain-containing proteins and is thus involved inphysiological processes in which one or more of these or other SH3domain-containing proteins are involved.

[0534] Human INTERCEPT 217 exhibits amino acid sequence similarity toporcine ribonuclease inhibitor, a protein which binds with high affinityto pancreatic ribonucleases and inhibits their activity. INTERCEPT 217thus is involved with similar physiological processes in humans. Analignment of the amino acid sequences of human INTERCEPT 217 and porcineribonuclease inhibitor protein (SwissProt Accession number P10775) isshown in FIG. 19G. In this alignment (made using the ALIGN software{Myers and Miller (1989) CABIOS, ver. 2.0}; pam120.mat scoring matrix;gap opening penalty=12, gap extension penalty=4), the proteins are 20.5%identical. An alignment of human (SEQ ID NO: 273) and murine INTERCEPT217 amino acid sequences (SEQ ID NO: 363; made using BESTFIT software,BLOSUM62 scoring matrix, gap opening penalty=12, frameshift gappenalty=5, gap extension penalty=4). In this alignment, the human andmurine amino acid sequences are 71.3% identical in the overlappingregion. Alignment of human and murine INTERCEPT 217 ORFs indicated 79.9%nucleotide sequence identity in the overlapping region.

[0535] The signal peptide prediction program SIGNALP (Nielsen et al.(1997) Protein Engineering 10:1-6) predicted that human INTERCEPT 217protein includes an approximately 20 (i.e., 18, 19, 20, 21, or 22) aminoacid residue signal peptide (amino acid residues 1 to 20 of SEQ ID NO:273; SEQ ID NO: 274) preceding the mature INTERCEPT 217 protein (i.e.,approximately amino acid residues 21 to 455 of SEQ ID NO: 273; SEQ IDNO: 275). In one embodiment, human INTERCEPT 217 protein includes anextracellular domain (amino acid residues 21 to 383 of SEQ ID NO: 273;SEQ ID NO: 276); a transmembrane domain (amino acid residues 384 to 403of SEQ ID NO: 273; SEQ ID NO: 277); and a cytoplasmic domain (amino acidresidues 404 to 455 of SEQ ID NO: 273; SEQ ID NO: 278). In analternative embodiment, human INTERCEPT 217 protein includes acytoplasmic domain (amino acid residues 21 to 383 of SEQ ID NO: 273; SEQID NO: 276); a transmembrane domain (amino acid residues 384 to 403 ofSEQ ID NO: 273; SEQ ID NO: 277); and an extracellular domain (amino acidresidues 404 to 455 of SEQ ID NO: 273; SEQ ID NO: 278).

[0536] The SIGNALP program predicted that murine INTERCEPT 217 proteinincludes an approximately 15 (i.e., 13, 14, 15, 16, or 17) amino acidresidue signal peptide (amino acid residues 1 to 16 of SEQ ID NO: 363;SEQ ID NO: 364) preceding the mature INTERCEPT 217 protein (i.e.,approximately amino acid residues 16 to 320 of SEQ ID NO: 363; SEQ IDNO: 365). In one embodiment, murine INTERCEPT 217 protein includes anextracellular domain (amino acid residues 16 to 213 of SEQ ID NO: 363;SEQ ID NO: 366); a transmembrane domain (amino acid residues 214 to 233of SEQ ID NO: 363; SEQ ID NO: 367); and a cytoplasmic domain (amino acidresidues 234 to 320 of SEQ ID NO: 363; SEQ ID NO: 368). In analternative embodiment, murine INTERCEPT 217 protein includes acytoplasmic domain (amino acid residues 16 to 213 of SEQ ID NO: 363; SEQID NO: 366); a transmembrane domain (amino acid residues 214 to 233 ofSEQ ID NO: 363; SEQ ID NO: 367); and an extracellular domain (amino acidresidues 234 to 320 of SEQ ID NO: 363; SEQ ID NO: 368).

[0537]FIG. 19F depicts a hydrophobicity plot of human INTERCEPT 217protein. Relatively hydrophobic regions are above the dashed horizontalline, and relatively hydrophilic regions are below the dashed horizontalline. The hydrophobic region which corresponds to amino acid residues 1to 20 of SEQ ID NO: 273 is the signal sequence of human INTERCEPT 217(SEQ ID NO: 274). The hydrophobic region which corresponds to amino acidresidues 384 to 403 of SEQ ID NO: 273 is the transmembrane domain ofhuman INTERCEPT 217 (SEQ ID NO: 277). As described elsewhere herein,relatively hydrophilic regions are generally located at or near thesurface of a protein, and are more frequently effective immunogenicepitopes than are relatively hydrophobic regions. For example, theregion of human INTERCEPT 217 protein from about amino acid residue 355to about amino acid residue 380 appears to be located at or near thesurface of the protein, while the region from about amino acid residue190 to about amino acid residue 210 appears not to be located at or nearthe surface. FIG. 19L depicts a hydrophobicity plot of murine INTERCEPT217 protein.

[0538] The predicted molecular weight of human INTERCEPT 217 proteinwithout modification and prior to cleavage of the signal sequence isabout 49.8 kilodaltons. The predicted molecular weight of the maturehuman INTERCEPT 217 protein without modification and after cleavage ofthe signal sequence is about 47.4 kilodaltons.

[0539] The predicted molecular weight of murine INTERCEPT 217 protein,without modification and prior to cleavage of the signal sequence isabout 35.5 kilodaltons. The predicted molecular weight of the maturehuman INTERCEPT 217 protein without modification and after cleavage ofthe signal sequence is about 33.8 kilodaltons.

[0540] Northern analysis experiments indicated that mRNA correspondingto the cDNA encoding INTERCEPT 217 is expressed in two forms, one havingan apparent approximate size of about 6 kilobases and another having anapparent approximate size of about 3 kilobases (i.e., corresponding tothe size of the INTERCEPT 217 cDNA). These experiments indicated thatINTERCEPT 217 is expressed in the tissues listed in Table XVII, wherein“++” indicates strong expression, “+” indicates lower expression, and“+/−” indicates still lower expression. TABLE XVII Animal TissueRelative Level of Expression Human pancreas ++ skeletal muscle + heart+/− brain +/− placenta +/− lung +/− liver +/− kidney +/−

[0541] An assay to detect possible secretion of INTERCEPT 217 proteinwas negative.

[0542] This assay was performed as described elsewhere in thisdisclosure.

[0543] Uses of INTERCEPT 217 Nucleic Acids,

[0544] Polypeptides, and Modulators Thereof

[0545] INTERCEPT 217 proteins are involved in disorders which affectboth tissues in which they are normally expressed and tissues in whichthey are normally not expressed. Based on the observation that INTERCEPT217 is expressed in pancreas, skeletal muscle, heart, brain, placenta,lung, liver, and kidney tissue, INTERCEPT 217 protein is involved in oneor more biological processes which occur in these tissues. Inparticular, INTERCEPT 217 is involved in modulating binding of cells ofone or more of these tissues with proteins of other cells or withsecreted proteins which occur in the extracellular environment of one ormore of these tissues. INTERCEPT 217 is especially implicated indisorders of skeletal muscle (e.g., protection of skeletal muscle cellsduring ischemia and in bruised tissue), and more especially thoseinvolving the pancreas (e.g., diabetes, pancreatitis, and the like).

[0546] Structural similarity of human INTERCEPT 217 protein with humanGP-IBa indicates that INTERCEPT 217 is involved in binding extracellularproteins and other ligands. INTERCEPT 217 protein is involved in bindingof proteins which induce release of pancreatic digestive enzymes (e.g.,amylases, lipases, proteases, and nucleases) from pancreatic cells, andin disorders associated with insufficient or inappropriate release ofsuch enzymes. INTERCEPT 217 protein is also involved in binding ofsecreted pancreatic digestive enzymes in pancreatic tissue, therebyprotecting pancreatic tissue from autodigestion. Thus, INTERCEPT 217protein is involved in disorders such as diabetes, pancreatitis, andpancreatic carcinoma which involve acute and chronic autodigestivedamage to pancreatic tissues. Homology of INTERCEPT 217 protein withporcine ribonuclease inhibitor protein is a further indication of thisinvolvement.

[0547] The presence of LRR domains in human INTERCEPT 217 protein anddetection of its expression in a variety of tissues indicate that thetissue protective functions of INTERCEPT 217 are not limited topancreatic tissues, but are involved in protection of other tissues aswell (e.g., skeletal muscle, heart, brain, placenta, lung, liver,prostate, and kidney tissues). INTERCEPT 217 is therefore involved inprotection of these (and likely other tissues) from the effects ofinflammation, autoimmunity, infection, and acute and chronic traumas.

[0548] Presence in INTERCEPT 217 protein of multiple SH3 domain bindingsites indicates that INTERCEPT 217 protein interacts with one or moreSH3 domain-containing proteins. Thus, INTERCEPT 217 protein mediatesbinding of proteins (i.e., binding of proteins to INTERCEPT 217 and toone another to form protein complexes) in cells in which it isexpressed. INTERCEPT 217 is also involved in transduction of signalsbetween the exterior environment of cells (i.e., including from othercells) and the interior of cells in which it is expressed. INTERCEPT 217mediates regulation of cell growth and proliferation, endocytosis,activation of respiratory burst, and other physiological processestriggered by transmission of a signal via a protein with which INTERCEPT217 interacts.

[0549] INTERCEPT 217-related molecules can be used to modulate one ormore of the activities in which INTERCEPT 217 is involved and can alsobe used to prevent, diagnose, or treat one or more of the disorders inwhich INTERCEPT 217 is involved.

[0550] INTERCEPT 217 polypeptides, nucleic acids, and modulatorsthereof, can, for example, be used to treat pancreatic disorders, suchas the pancreatic disorders described elsewhere in this disclosure.INTERCEPT 217 polypeptides, nucleic acids, and modulators thereof can beused to prognosticate, diagnose, inhibit, prevent, or alleviate one ormore of these disorders.

[0551] In another example, INTERCEPT 217 polypeptides, nucleic acids,and modulators thereof, can be used to treat disorders of skeletalmuscle, such as the skeletal muscle disorders described elsewhere inthis disclosure. INTERCEPT 217 polypeptides, nucleic acids, andmodulators thereof can be used to prognosticate, diagnose, inhibit,prevent, or alleviate one or more of these disorders.

[0552] Because INTERCEPT 217 exhibits expression in heart tissue,INTERCEPT 217 nucleic acids, proteins, and modulators thereof can beused to treat disorders such as the cardiovascular disorders describedelsewhere in this disclosure. INTERCEPT 217 polypeptides, nucleic acids,and modulators thereof can be used to prognosticate, diagnose, inhibit,prevent, or alleviate one or more of these disorders.

[0553] In another example, INTERCEPT 217 polypeptides, nucleic acids,and modulators thereof, can be used to treat disorders of the brain,such as the brain disorders described elsewhere in this disclosure.INTERCEPT 217 polypeptides, nucleic acids, and modulators thereof can beused to prognosticate, diagnose, inhibit, prevent, or alleviate one ormore of these disorders.

[0554] In another example, INTERCEPT 217 polypeptides, nucleic acids,and modulators thereof, can be used to treat placental disorders, suchas toxemia of pregnancy (e.g., preeclampsia and eclampsia), placentitis,and spontaneous abortion. INTERCEPT 217 polypeptides, nucleic acids, andmodulators thereof can be used to prognosticate, diagnose, inhibit,prevent, or alleviate one or more of these disorders.

[0555] In another example, INTERCEPT 217 polypeptides, nucleic acids,and modulators thereof, can be used to treat pulmonary (i.e., lung)disorders, such as atelectasis, cystic fibrosis, rheumatoid lungdisease, pulmonary congestion, pulmonary edema, chronic obstructiveairway disease (e.g., emphysema, chronic bronchitis, bronchial asthma,and bronchiectasis), diffuse interstitial diseases (e.g., sarcoidosis,pneumoconiosis, hypersensitivity pneumonitis, Goodpasture's syndrome,idiopathic pulmonary hemosiderosis, pulmonary alveolar proteinosis,desquamative interstitial pneumonitis, chronic interstitial pneumonia,fibrosing alveolitis, hamman-rich syndrome, pulmonary eosinophilia,diffuse interstitial fibrosis, Wegener's granulomatosis, lymphomatoidgranulomatosis, and lipid pneumonia), and tumors (e.g., bronchogeniccarcinoma, bronchioloalveolar carcinoma, bronchial carcinoid, hamartoma,and mesenchymal tumors). INTERCEPT 217 polypeptides, nucleic acids, andmodulators thereof can be used to prognosticate, diagnose, inhibit,prevent, or alleviate one or more of these disorders.

[0556] In yet another example, INTERCEPT 217 polypeptides, nucleicacids, and modulators thereof, can be used to treat hepatic (i.e.,liver) disorders, such as the liver disorders described elsewhere inthis disclosure. INTERCEPT 217 polypeptides, nucleic acids, andmodulators thereof can be used to prognosticate, diagnose, inhibit,prevent, or alleviate one or more of these disorders.

[0557] In still another example, INTERCEPT 217 polypeptides, nucleicacids, and modulators thereof, can be used to treat renal (i.e., kidney)disorders, such as the kidney disorders described elsewhere in thisdisclosure. INTERCEPT 217 polypeptides, nucleic acids, and modulatorsthereof can be used to prognosticate, diagnose, inhibit, prevent, oralleviate one or more of these disorders.

[0558] INTERCEPT 297

[0559] A cDNA clone (designated jthsa085g01) encoding at least a portionof human INTERCEPT 297 protein was isolated from a human fetal spleencDNA library. The human INTERCEPT 297 protein is predicted by structuralanalysis to be a transmembrane protein.

[0560] The full length of the cDNA encoding human INTERCEPT 297 protein(FIG. 20; SEQ ID NO: 279) is 1518 nucleotide residues. The ORF of thiscDNA, nucleotide residues 40 to 1152 of SEQ ID NO: 279 (i.e., SEQ ID NO:280), encodes a 371-amino acid transmembrane protein (FIG. 20; SEQ IDNO: 281).

[0561] The invention thus includes purified human INTERCEPT 297 protein,both in the form of a 371 amino acid residue protein (SEQ ID NO: 281) inwhich the ‘signal sequence’ (i.e., the portion of INTERCEPT 297 proteincorresponding to amino acid residues 1 to 18) described in this sectionis not cleaved and in the form of a 353 amino acid residue protein (SEQID NO: 283) in which the ‘signal sequence’ is cleaved. Human INTERCEPT297 protein can exist with or without the signal sequence polypeptide atthe amino terminus thereof. It is likely that the ‘signal sequence’ isnot cleaved, but is instead a transmembrane domain of the protein.

[0562] The invention includes nucleic acid molecules which encode anINTERCEPT 297 polypeptide of the invention. Such nucleic acids include,for example, a DNA molecule having the nucleotide sequence listed in SEQID NO: 279 or some portion thereof, such as the portion which encodesmature INTERCEPT 297 protein, immature INTERCEPT 297 protein, or adomain of INTERCEPT 297 protein. These nucleic acids are collectivelyreferred to as INTERCEPT 297 nucleic acids of the invention.

[0563] INTERCEPT 297 proteins and nucleic acid molecules encoding themcomprise a family of molecules having certain conserved structural andfunctional features.

[0564] A common domain present in INTERCEPT 297 proteins is a signalsequence.

[0565] In one embodiment, a INTERCEPT 297 protein contains a signalsequence corresponding to about amino acid residues 1 to 18 of SEQ IDNO: 281 (SEQ ID NO: 282). The signal sequence can be cleaved duringprocessing of the mature protein, but it is likely that amino acidresidues 1 to 18 of SEQ ID NO: 281 represent a (non-cleaved)transmembrane region of the protein.

[0566] INTERCEPT 297 proteins can include one or more extracellulardomains. In one embodiment of the human INTERCEPT 297 protein,extracellular domains are located from about amino acid residues 19 to47, from about amino acid residues 110 to 118, from about amino acidresidues 162 to 175, from about amino acid residues 234 to 260, and fromabout amino acid residues 313 to 319 of SEQ ID NO: 281 (SEQ ID NOs:284-288, respectively). In an alternative embodiment, extracellulardomains are located from about amino acid residue 69 to 88, from aboutamino acid residue 138 to 144, from about amino acid residue 193 to 215,from about amino acid residue 284 to 292, and from about amino acidresidue 337 to 371 of SEQ ID NO: 281 (SEQ ID NOs: 298-302,respectively).

[0567] In addition, INTERCEPT 297 includes one or more transmembranedomains.

[0568] In one embodiment, a INTERCEPT 297 protein of the inventioncontains transmembrane domains corresponding to about amino acidresidues 48 to 68, about amino acid residues 89 to 109, about amino acidresidues 119 to 137, about amino acid residues 145 to 161, about aminoacid residues 176 to 192, about amino acid residues 216 to 233, aboutamino acid residues 261 to 283, about amino acid residues 293 to 312,and about amino acid residues 320 to 336 of SEQ ID NO: 281 (SEQ ID NOs:289-297, respectively). As indicated above, it is likely that the‘signal sequence’ of INTERCEPT 297 is an additional (and non-cleaved)transmembrane region.

[0569] The present invention includes INTERCEPT 297 proteins having oneor more cytoplasmic domains. In one embodiment of the human INTERCEPT297 protein, cytoplasmic domains are located from about amino acidresidue 69 to 88, from about amino acid residue 138 to 144, from aboutamino acid residue 193 to 215, from about amino acid residue 284 to 292,and from about amino acid residue 337 to 371 of SEQ ID NO: 281 (SEQ IDNOs: 298-302, respectively). In an alternative embodiment, cytoplasmicdomains are located from about amino acid residues 19 to 47, from aboutamino acid residues 110 to 118, from about amino acid residues 162 to175, from about amino acid residues 234 to 260, and from about aminoacid residues 313 to 319 of SEQ ID NO: 281 (SEQ ID NOs: 284-288,respectively).

[0570] INTERCEPT 297 proteins typically comprise a variety of potentialpost-translational modification sites (often within an extracellulardomain), such as those described herein in Table XVIII, as predicted bycomputerized sequence analysis of INTERCEPT 297 proteins using aminoacid sequence comparison software (comparing the amino acid sequence ofINTERCEPT 297 with the information in the PROSITE database {rel. 12.2;February 1995} and the Hidden Markov Models database {Rel. PFAM 3.3}).In certain embodiments, a protein of the invention has at least 1, 2, 4,6, 10, 15, or 20 or more of the post-translational modification siteslisted in Table XVIII. TABLE XVIII Amino Acid Type of PotentialModification Site Residues Amino Acid or Domain of SEQ ID NO: 281Sequence N-glycosylation site 110 to 113 NMTS 269 to 272 NISS Proteinkinase C phosphorylation site  24 to 26 SAK 290 to 292 TTR 297 to 299SLR Casein kinase II phosphorylation site  78 to 81 SSVD 165 to 168 SKHD245 to 248 TLED 354 to 357 SEQE N-myristoylation site  18 to 23 GSINTL 35 to 40 GCGGSK  53 to 58 GMFLGE  74 to 79 GQSDSS 147 to 152 GILATI 236to 241 GSFSGN 268 to 273 GNISSI 280 to 285 GISVTK Amidation site 136 to139 LGRR DUF6 domain  44 to 171 See FIG. 20

[0571] In one embodiment, the protein of the invention has at least onedomain that is at least 55%, preferably at least about 65%, morepreferably at least about 75%, yet more preferably at least about 85%,and most preferably at least about 95% identical to this DUF6 domain.

[0572] The DUF6 domain is a transmembrane domain that is highlyconserved among eukaryote, prokaryote, and archae kingdoms. This highdegree of domain sequence conservation indicates that proteins of theclass which includes INTERCEPT 297 are involved in fundamental membranephysiology of living cells. INTERCEPT 297 protein is therefore involvedin disorders which are associated with aberrant membrane functionincluding, for example, disorders involving abnormal membrane fluidity,disorders involving aberrant transmembrane transport, disordersinvolving abnormal membrane organization, disorders involving abnormalmembrane synthesis, disorders involving aberrant cell division, and thelike.

[0573] The signal peptide prediction program SIGNALP (Nielsen et al.(1997) Protein Engineering 10:1-6) predicted that human INTERCEPT 297protein includes an approximately 18 (i.e., 16, 17, 18, 19, or 20) aminoacid residue signal peptide (amino acid residues 1 to 18 of SEQ ID NO:281; SEQ ID NO: 282) preceding the mature INTERCEPT 297 protein (i.e.,approximately amino acid residues 19 to 371 of SEQ ID NO: 281; SEQ IDNO: 283). In one embodiment, human INTERCEPT 297 protein includes aboutfive extracellular domains (amino acid residues 19 to 47, 110 to 118,162 to 175, 234 to 260, and 313 to 319 of SEQ ID NO: 281); about ninetransmembrane domains (amino acid residues 48 to 68, 89 to 109, 119 to137, 145 to 161, 176 to 192, 216 to 233, 261 to 283, 293 to 312, and 320to 326 of SEQ ID NO: 281); and about five cytoplasmic domains (aminoacid residues 69 to 88, 138 to 144, 193 to 215, 284 to 292, and 337 to371 of SEQ ID NO: 281). In an alternative embodiment, human INTERCEPT297 protein includes about five cytoplasmic domains (amino acid residues19 to 47, 110 to 118, 162 to 175, 234 to 260, and 313 to 319 of SEQ IDNO: 281); about nine transmembrane domains (amino acid residues 48 to68, 89 to 109, 119 to 137, 145 to 161, 176 to 192, 216 to 233, 261 to283, 293 to 312, and 320 to 326 of SEQ ID NO: 281); and about fiveextracellular domains (amino acid residues 69 to 88, 138 to 144, 193 to215, 284 to 292, and 337 to 371 of SEQ ID NO: 281).

[0574]FIG. 20D depicts a hydrophobicity plot of human INTERCEPT 297protein.

[0575] Relatively hydrophobic regions are above the dashed horizontalline, and relatively hydrophilic regions are below the dashed horizontalline. Hydrophobic region corresponding to the signal sequence and thetransmembrane domains are observed in this figure. As describedelsewhere herein, relatively hydrophilic regions are generally locatedat or near the surface of a protein, and are more frequently effectiveimmunogenic epitopes than are relatively hydrophobic regions. Forexample, the region of human INTERCEPT 297 protein from about amino acidresidue 165 to about amino acid residue 175 appears to be located at ornear the surface of the protein.

[0576] The predicted molecular weight of human INTERCEPT 297 proteinwithout modification and prior to cleavage of the signal sequence isabout 40.2 kilodaltons. The predicted molecular weight of the maturehuman INTERCEPT 297 protein without modification and after cleavage ofthe signal sequence is about 38.2 kilodaltons.

[0577] Uses of INTERCEPT 297 Nucleic Acids,

[0578] Polypeptides, and Modulators Thereof

[0579] INTERCEPT 297 proteins are involved in disorders which affectboth tissues in which they are normally expressed and tissues in whichthey are normally not expressed. Based on the observation that INTERCEPT297 is expressed in human fetal spleen, INTERCEPT 297 protein isinvolved in one or more biological processes which occur in fetal andspleen tissues. In particular, INTERCEPT 297 is involved in modulatinggrowth, proliferation, survival, differentiation, and activity of cellsincluding, but not limited to, spleen and fetal cells of the animal inwhich it is normally expressed. Thus, INTERCEPT 297 has a role indisorders which affect these cells and their growth, proliferation,survival, differentiation, and activity (e.g., hematologic and immunedisorders). Expression of INTERCEPT 297 in an animal is also involved inmodulating growth, proliferation, survival, differentiation, andactivity of cells and viruses which are foreign to the host (i.e.,bacterial, fungal, and viral infections).

[0580] INTERCEPT 297 bears amino acid sequence similarity toCaenorhabditis elegans protein C2G12.12, and therefore exhibits one ormore activities analogous to that protein.

[0581] INTERCEPT 297 nucleic acids, proteins, and modulators thereof canbe used to modulate proliferation, migration, morphology,differentiation, function, or some combination of these, of cells thatform the spleen, (e.g., cells of the splenic connective tissue, splenicsmooth muscle cells, or endothelial cells of the splenic blood vessels)or of blood cells that are processed. (e.g., regenerated, matured, orphagocytized) within the spleen, as described elsewhere in thisdisclosure. INTERCEPT 297 polypeptides, nucleic acids, and modulatorsthereof can be used to prognosticate, diagnose, inhibit, prevent, oralleviate one or more of these disorders.

[0582] Structural analysis of INTERCEPT 297 and the presence of a DUF6domain therein indicate that INTERCEPT 297 is involved in disorderswhich affect membrane structure and function. INTERCEPT 297 can be usedto affect development and persistence of disorders involvinginappropriate membrane structure and function, such as atherogenesis,arteriosclerosis, and various transmembrane transport disorders.

[0583] Other examples of disorders for which INTERCEPT 297 is usefulinclude disorders involving generation and persistence of an immuneresponse to bacterial, fungal, and viral infections. INTERCEPT 297polypeptides, nucleic acids, and modulators thereof can be used toprognosticate, diagnose, inhibit, prevent, or alleviate one or more ofthese disorders.

[0584] The structure of INTERCEPT 297 is analogous to the structures ofintegral membrane proteins responsible for transmembrane transport ofmolecules such as sugars, ions, and the like. INTERCEPT 297 is thusinvolved in one or more transmembrane transport-related disorders suchas cystic fibrosis, nerve conduction disorders (e.g., pain and loss orfailure of sensation), muscle contraction disorders (e.g., cardiacinsufficiency), metal ion uptake disorders (e.g., hemochromatosis), andthe like. INTERCEPT 297 polypeptides, nucleic acids, and modulatorsthereof can be used to prognosticate, diagnose, inhibit, prevent, oralleviate one or more of these disorders.

[0585] TANGO 276

[0586] A cDNA clone (designated jthsa006e01) encoding at least a portionof human TANGO 276 protein was isolated from a human fetal spleen cDNAlibrary. The human TANGO 276 protein is predicted by structural analysisto be a secreted protein.

[0587] The full length of the cDNA encoding human TANGO 276 protein(FIG. 21; SEQ ID NO: 303) is 2811 nucleotide residues. The ORF of thiscDNA, nucleotide residues 58 to 786 of SEQ ID NO: 303 (i.e., SEQ ID NO:304), encodes a 243-amino acid secreted protein (FIG. 21; SEQ ID NO:305).

[0588] The invention thus includes purified human TANGO 276 protein,both in the form of the immature 243 amino acid residue protein (SEQ IDNO: 305) and in the form of the mature, approximately 223 amino acidresidue protein (SEQ ID NO: 307). Mature human TANGO 276 protein can besynthesized without the signal sequence polypeptide at the aminoterminus thereof, or it can be synthesized by generating immature TANGO276 protein and cleaving the signal sequence therefrom.

[0589] The invention includes nucleic acid molecules which encode aTANGO 276 polypeptide of the invention. Such nucleic acids include, forexample, a DNA molecule having the nucleotide sequence listed in SEQ IDNO: 303 or some portion thereof, such as the portion which encodesmature TANGO 276 protein, immature TANGO 276 protein, or a domain ofTANGO 276 protein. These nucleic acids are collectively referred to asTANGO 276 nucleic acids of the invention.

[0590] TANGO 276 proteins and nucleic acid molecules encoding themcomprise a family of molecules having certain conserved structural andfunctional features, as indicated by the conservation of amino acidsequence between human TANGO 276 protein and the murine proteindesignated M-Sema-F (see Inagaki et al. (1995) FEBS Lett. 370:269-272),as shown in FIGS. 21F to 21H.

[0591] A common domain present in TANGO 276 proteins is a signalsequence. In one embodiment, a TANGO 276 protein contains a signalsequence corresponding to about amino acid residues 1 to 20 of SEQ IDNO: 305 (SEQ ID NO: 306). The signal sequence is cleaved duringprocessing of the mature protein.

[0592] TANGO 276 proteins can exist in a secreted form, such as a matureprotein having the amino acid sequence of amino acid residues 21 to 243of SEQ ID NO: 305 (SEQ ID NO: 307).

[0593] TANGO 276 proteins typically comprise a variety of potentialpost-translational modification sites (often within an extracellulardomain), such as those described herein in Table XIX, as predicted bycomputerized sequence analysis of TANGO 276 proteins using amino acidsequence comparison software (comparing the amino acid sequence of TANGO276 with the information in the PROSITE database {rel. 12.2; February1995} and the Hidden Markov Models database {Rel. PFAM 3.3}). In certainembodiments, a protein of the invention has at least 1, 2, 4, 6, or all8 of the post-translational modification sites listed in Table XIX.TABLE XIX Amino Acid Type of Potential Modification Site Residues AminoAcid or Domain of SEQ ID NO: 305 Sequence N-glycosylation site 106 to109 NQTE 121 to 124 NASH cAMP- or cGMP-dependent protein 43 to 46 RRFSkinase phosphorylation site Protein kinase C phosphorylation site 194 to196 SLK Casein kinase II phosphorylation site 34 to 37 SSGE 57 to 60TLTE N-myristoylation site 16 to 21 GLGIGA 68 to 73 GAREAL Sema domain 53 to 141 See FIG. 21

[0594] A Sema domain occurs in human TANGO 276 protein. In oneembodiment, the protein of the invention has at least one domain that isat least 55%, preferably at least about 65%, more preferably at leastabout 75%, yet more preferably at least about 85%, and most preferablyat least about 95% identical to this Sema domain.

[0595] Sema domains occur in semaphorin proteins. Semaphorins are alarge family of secreted and transmembrane proteins, some of whichfunction as repellent signals during neural axon guidance. The Semadomain and a variety of semaphorin proteins in which it occurs aredescribed, for example, in Winberg et al. (1998 Cell 95:903-916). Semadomains also occur in human hepatocyte growth factor receptor (SwissProtAccession no. P08581) and the similar neuronal and epithelialtransmembrane receptor protein (SwissProt Accession no. P51805). Thepresence of a Sema domain in human TANGO 276 protein indicates thatTANGO 276 is involved in one or more physiological processes in whichthe semaphorins are involved, has biological activity in common with oneor more of the semaphorins, or both.

[0596] Human TANGO 276 protein exhibits considerable sequence similarityto murine M-Sema F protein (GenBank Accession no. S79463), as indicatedherein in FIGS. 21F to 21H. FIGS. 21F to 21H depict an alignment of theamino acid sequences of human TANGO 276 protein (SEQ ID NO: 305) andmurine M-Sema F protein (SEQ ID NO: 335). In this alignment (pam120.matscoring matrix, gap opening penalty=12, gap extension penalty=4), theamino acid sequences of the proteins are 76.1% identical. FIGS. 211through 21R depict an alignment of the nucleotide sequences of cDNAencoding human TANGO 276 protein (SEQ ID NOs: 303) and murine cDNAencoding M-Sema F protein (SEQ ID NO: 336). In this alignment(pam120.mat scoring matrix, gap opening penalty=12, gap extensionpenalty=4), the nucleic acid sequences of the cDNAs are 79.7% identical.Thus, TANGO 276 is related to murine M-Sema F and shares functionalsimilarities to that protein.

[0597] It is known that semaphorins are bi-functional, capable offunctioning either as attractive axonal guidance proteins or asrepellent axonal guidance proteins (Wong et al. (1997) Development124:3597-3607). Furthermore, semaphorins bind with neuronal cell surfaceproteins designated plexins, which are expressed on both neuronal cellsand cells of the immune system (Comeau et al. (1998) Immunity 8:473-482;Jin and Strittmatter (1997) J. Neurosci. 17:6256-6263).

[0598] The signal peptide prediction program SIGNALP (Nielsen et al.(1997) Protein Engineering 10:1-6) predicted that human TANGO 276protein includes an approximately 20 (i.e., 18, 19, 20, 21, or 22) aminoacid signal peptide (amino acid residues 1 to 20 of SEQ ID NO: 305; SEQID NO: 306) preceding the mature TANGO 276 protein (i.e., approximatelyamino acid residues 21 to 243 of SEQ ID NO: 304; SEQ ID NO: 307). HumanTANGO 276 protein is a secreted protein.

[0599]FIG. 21E depicts a hydrophobicity plot of human TANGO 276 protein.

[0600] Relatively hydrophobic regions are above the dashed horizontalline, and relatively hydrophilic regions are below the dashed horizontalline. The hydrophobic region which corresponds to about amino acidresidues 1 to 20 of SEQ ID NO: 305 is the signal sequence of human TANGO276. As described elsewhere herein, relatively hydrophilic regions aregenerally located at or near the surface of a protein, and are morefrequently effective immunogenic epitopes than are relativelyhydrophobic regions. For example, the region of human TANGO 276 proteinfrom about amino acid residue 90 to about amino acid residue 105 appearsto be located at or near the surface of the protein, while the regionfrom about amino acid residue 170 to about amino acid residue 180appears not to be located at or near the surface.

[0601] The predicted molecular weight of human TANGO 276 protein withoutmodification and prior to cleavage of the signal sequence is about 27.1kilodaltons. The predicted molecular weight of the mature human TANGO276 protein without modification and after cleavage of the signalsequence is about 24.8 kilodaltons.

[0602] Northern analysis experiments indicated that mRNA correspondingto the cDNA encoding TANGO 276 is expressed in the tissues listed inTable XX, wherein “++” indicates a greater level of expression and “+”indicates a lower level of expression. TABLE XX Animal Tissue RelativeLevel of Expression Human heart ++ placenta ++ brain + lung + liver +skin + kidney + pancreas +

[0603] Uses of TANGO 276 Nucleic Acids,

[0604] Polypeptides, and Modulators Thereof

[0605] TANGO 276 proteins are involved in disorders which affect bothtissues in which they are normally expressed and tissues in which theyare normally not expressed. Based on the observation that TANGO 276 isexpressed in human heart and placenta tissues, to a lesser extent inbrain, lung, liver, skin, kidney, and pancreas tissues, and in fetalspleen tissue, TANGO 276 protein is involved in one or more biologicalprocesses which occur in these tissues. In particular, TANGO 276 isinvolved in modulating growth, proliferation, survival, differentiation,and activity of cells including, but not limited to, heart, placenta,spleen, brain, lung, liver, skin, kidney, and pancreas cells of theanimal in which it is normally expressed. Thus, TANGO 276 has a role indisorders which affect these cells and their growth, proliferation,survival, differentiation, and activity.

[0606] Because TANGO 276 exhibits expression in the heart, TANGO 276nucleic acids, proteins, and modulators thereof can be used to treatcardiovascular disorders, such as those described elsewhere in thisdisclosure. TANGO 276 polypeptides, nucleic acids, or modulators thereofcan be used to prognosticate, diagnose, inhibit, prevent, or alleviateone or more of these disorders.

[0607] In another example, TANGO 276 polypeptides, nucleic acids, andmodulators thereof can be used to treat placental disorders, such asthose described elsewhere in this disclosure. TANGO 276 polypeptides,nucleic acids, and modulators thereof can be used to prognosticate,diagnose, inhibit, prevent, or alleviate one or more of these disorders.

[0608] In another example, TANGO 276 polypeptides, nucleic acids, ormodulators thereof, can be used to treat disorders of the brain, such asthe brain disorders described elsewhere in this disclosure. TANGO 276polypeptides, nucleic acids, and modulators thereof can be used toprognosticate, diagnose, inhibit, prevent, or alleviate one or more ofthese disorders.

[0609] TANGO 276 polypeptides, nucleic acids, and modulators thereof canbe associated with pulmonary (i.e., lung) disorders, such as thepulmonary disorders described elsewhere in this disclosure. TANGO 276polypeptides, nucleic acids, or modulators thereof can be used toprognosticate, diagnose, inhibit, prevent, or alleviate one or more ofthese disorders.

[0610] In another example, TANGO 276 polypeptides, nucleic acids, andmodulators thereof, can be used to treat hepatic (i.e., liver)disorders, such as the liver disorders described elsewhere in thisdisclosure. TANGO 276 polypeptides, nucleic acids, and modulatorsthereof can be used to prognosticate, diagnose, inhibit, prevent, oralleviate one or more of these disorders.

[0611] Examples of skin disorders with which TANGO 276 can be associatedinclude those described elsewhere in this disclosure. TANGO 276proteins, nucleic acids encoding them, and agents that modulate activityor expression of either of these can be used to prognosticate, diagnose,treat, and inhibit one or more of these disorders.

[0612] In another example, TANGO 276 polypeptides, nucleic acids, ormodulators thereof, can be used to treat renal (i.e., kidney) disorders,such as the kidney disorders described elsewhere in this disclosure.TANGO 276 polypeptides, nucleic acids, and modulators thereof can beused to prognosticate, diagnose, inhibit, prevent, or alleviate one ormore of these disorders.

[0613] Pancreatic disorders in which TANGO 276 can be involved includethe pancreatic disorders described elsewhere in this disclosure. TANGO276 polypeptides, nucleic acids, or modulators thereof can be used toprognosticate, diagnose, inhibit, prevent, or alleviate one or more ofthese disorders.

[0614] The presence of the Sema domain in TANGO 276 indicates that thisprotein is involved in development of neuronal and epithelial tissuesand also functions as a repellant protein which guides axonaldevelopment. TANGO 276 modulates nerve growth and regeneration and alsomodulates growth and regeneration of other epithelial tissues. TANGO 276is thus involved in a variety of neuronal disorder including, but notlimited to, one or more of seizure, epilepsy, (regeneration of) neuronaldamage, pain (including, for example, migraine, headache, and otherchronic pain), infections of the central nervous system, multiplesclerosis, sleep disorders, psychological disorders, nerve rootdisorders, and the like. Presence of a Sema domain in TANGO 276 furtherindicates that TANGO 276 has one or more physiological roles in commonwith other proteins (e.g., secreted and transmembrane semaphorins,collapsing, neuropilins, plexins, and the like) in which the Sema domainoccurs. Thus, TANGO 276 is implicated in development, maintenance, andregeneration of neuronal connections and networks, in modulatingdifferentiation of cells of the immune system, in modulating cytokineproduction by cells of the immune system, in modulating reactivity ofcells of the immune system toward cytokines, in modulating initiationand persistence of an inflammatory response, and in modulatingproliferation of epithelial cells. Sema domain-containing proteins havealso been implicated in development and progression of small cell lungcancer, in normal brain development, and immune system regulation. Thisindicates that TANGO 276 is also involved in one or more of theseprocesses and in disorders relating to these processes (e.g., small celllung cancer, brain development disorders, and immune and auto-immunedisorders). TANGO 276 polypeptides, nucleic acids, and modulatorsthereof can be used to prognosticate, diagnose, inhibit, prevent, oralleviate one or more of these disorders.

[0615] The observation that TANGO 276 shares identity with the murinesemaphorin protein designated M-Sema F suggests that TANGO 276 hasactivity identical or analogous to the activity of this protein. Theseobservations indicate that TANGO 276 modulates growth, proliferation,survival, differentiation, and activity of neuronal cells. Thus, TANGO276 protein is useful, for example, for modulating and guiding neuralaxon development and for modulating establishment and maintenance ofneuronal networks.

[0616] TANGO 292

[0617] A cDNA clone (designated jthkf040b11) encoding at least a portionof human TANGO 292 protein was isolated from a human normal embryonickeratinocyte cDNA library. A corresponding gerbil cDNA clone (designatedjtiba040e12) was also isolated, and encoded at least a portion of gerbilTANGO 292 protein. The human and TANGO 292 proteins are predicted bystructural analysis to be transmembrane proteins.

[0618] The full length of the cDNA encoding human TANGO 292 protein(FIG. 22; SEQ ID NO: 308) is 2498 nucleotide residues. The ORF of thiscDNA, nucleotide residues 205 to 882 of SEQ ID NO: 308 (i.e., SEQ ID NO:309), encodes a 226-amino acid residue transmembrane protein (FIG. 22;SEQ ID NO: 310). The full length of the cDNA encoding gerbil TANGO 292protein (FIG. 22; SEQ ID NO: 351) is 2002 nucleotide residues. The ORFof this cDNA, nucleotide residues 89 to 763 of SEQ ID NO: 351 (i.e., SEQID NO: 352), encodes a 225-amino acid transmembrane protein (FIG. 22;SEQ ID NO: 353).

[0619] The invention thus includes purified human TANGO 292 protein,both in the form of the immature 226 amino acid residue protein (SEQ IDNO: 310) and in the form of the mature, approximately 209 amino acidresidue protein (SEQ ID NO: 312).

[0620] The invention also includes purified gerbil TANGO 292 protein,both in the form of the immature 225-amino acid residue (SEQ ID NO: 353)protein and in the form of the mature, approximately 208-amino acidresidue protein (SEQ ID NO: 355). Mature human or gerbil TANGO 292protein can be synthesized without the signal sequence polypeptide atthe amino terminus thereof, or it can be synthesized by generatingimmature TANGO 292 protein and cleaving the signal sequence therefrom.

[0621] The invention includes nucleic acid molecules which encode aTANGO 292 polypeptide of the invention. Such nucleic acids include, forexample, a DNA molecule having the nucleotide sequence listed in SEQ IDNO: 308 or 351 or some portion thereof, such as the portion whichencodes mature human or gerbil TANGO 292 protein, immature human orgerbil TANGO 292 protein, or a domain of human or gerbil TANGO 292protein. These nucleic acids are collectively referred to as TANGO 292nucleic acids of the invention.

[0622] TANGO 292 proteins and nucleic acid molecules encoding themcomprise a family of molecules having certain conserved structural andfunctional features. This family includes, for example, human and gerbilTANGO 292 proteins and nucleic acid molecules described herein.

[0623] A common domain present in TANGO 292 proteins is a signalsequence. In one embodiment, a TANGO 292 protein contains a signalsequence corresponding to about amino acid residues 1 to 17 of SEQ IDNO: 310 (SEQ ID NO: 311) or to about amino acid residues 1 to 17 of SEQID NO: 353 (SEQ ID NO: 354). The signal sequence is cleaved duringprocessing of the mature protein.

[0624] TANGO 292 proteins can include an extracellular domain. The humanTANGO 292 protein extracellular domain is located from about amino acidresidue 18 to about amino acid residue 113 of SEQ ID NO: 310 (SEQ ID NO:313). The gerbil TANGO 292 protein extracellular domain includes atleast about amino acid residues 18 to 112 of SEQ ID NO: 353 (SEQ ID NO:356).

[0625] In addition, TANGO 292 include a transmembrane domain. In oneembodiment, a human TANGO 292 protein contains a transmembrane domaincorresponding to about amino acid residues 114 to 138 of SEQ ID NO: 310(SEQ ID NO: 314). Gerbil TANGO 292 protein includes a transmembranedomain corresponding to about amino acid residues 113 to 137 of SEQ IDNO: 353 (SEQ ID NO: 357).

[0626] The present invention includes TANGO 292 proteins having acytoplasmic domain, particularly including proteins having acarboxyl-terminal cytoplasmic domain. The human TANGO 292 cytoplasmicdomain is located from about amino acid residue 139 to amino acidresidue 226 of SEQ ID NO: 310 (SEQ ID NO: 315).

[0627] The gerbil TANGO 292 cytoplasmic domain is located from aboutamino acid residue 138 to amino acid residue 225 of SEQ ID NO: 353 (SEQID NO: 358).

[0628] TANGO 292 proteins typically comprise a variety of potentialpost-translational modification sites (often within an extracellulardomain), such as those described herein in Table XXIa as predicted bycomputerized sequence analysis of human TANGO 292 protein, or in TableXXIb as predicted by computerized sequence analysis of gerbil TANGO 292protein, using amino acid sequence comparison software (comparing theamino acid sequence of TANGO 292 with the information in the PROSITEdatabase {rel. 12.2; February 1995} and the Hidden Markov Modelsdatabase {Rel. PFAM 3.3}). In certain embodiments, a protein of theinvention has at least 1, 2, 4, 6, or all of the post-translationalmodification sites listed in Table XXIa or in Table XXIb. TABLE XXIaType of Potential Amino Acid Modification Site Residues of Amino Acid orDomain SEQ ID NO: 310 Sequence cAMP-or cGMP-dependent protein 197 to 200RKHS kinase phosphorylation site Protein kinase C phosphorylation site37 to 39 TSK 97 to 99 SAK 102 to 104 TTK 196 to 198 TRK Casein kinase IIphosphorylation site 37 to 40 TSKE 103 to 106 TKSD 180 to 183 SVEDN-myristoylation site 116 to 121 GLLTGL Vitamin K-dependentcarboxylation 56 to 98 See FIG. 22 domain

[0629] TABLE XXIb Amino Acid Type of Potential Modification Residues ofAmino Acid Site or Domain SEQ ID NO: 353 Sequence cAMP-or cGMP-dependentprotein 196 to 199 RKHS kinase phosphorylation site Protein kinase Cphosphorylation site 23 to 25 SLK 37 to 39 SKK 96 to 98 SVK 101 to 103TTR 155 to 157 TRR 195 to 197 TRK Casein kinase II phosphorylation site74 to 77 SYEE 102 to 105 TRSD 155 to 157 THEE 195 to 197 SSSEN-myristoylation site 33 to 38 GVFASK 115 to 120 GLLTGL VitaminK-dependent carboxylation 55 to 92 See FIG. 22 domain

[0630] Among the domains that occur in TANGO 292 protein is a vitaminK-dependent carboxylation domain. In one embodiment, the protein of theinvention has at least one domain that is at least 55%, preferably atleast about 65%, more preferably at least about 75%, yet more preferablyat least about 85%, and most preferably at least about 95% identical tothis vitamin K-dependent carboxylation domain.

[0631] The vitamin K-dependent carboxylation domain has the followingconsensus sequence (SEQ ID NO: 454), wherein standard single-letteramino acid codes are used and ‘X’ refers to any amino acid residue.—X₁₂-E-X₃-E-X—C—X₆-(D or E or N)—X-(L or I or V or M or F or Y)-Xg-(F orY or W)-Glutamic acid residues within this consensus region arepotential vitamin K-dependent carboxylation sites. Human TANGO 292 has 9glutamic acid residues in the vitamin K-dependent carboxylation domainlocated from about amino acid residue 56 to 98 of SEQ ID NO: 310, namelyat amino acid residues 58, 66, 68, 71, 72, 77, 78, 81, and 86 of SEQ IDNO: 310, and gerbil TANGO 292 has 10 glutamic acid residues in thevitamin K-dependent carboxylation domain located from about amino acidresidue 55 to 92 of SEQ ID NO: 353, namely at amino acid residues 57,65, 67, 70, 71, 76, 77, 80, 86, and 87 of SEQ ID NO: 353. In oneembodiment, the protein of the invention is carboxylated at one or moreof these glutamic acid residues. In some proteins in which a vitaminK-dependent carboxylation domain occurs, many of the glutamic acidresidues which occur from the amino terminus of the protein through theconserved aromatic residue at the carboxyl terminal end of the domainare carboxylated. Human TANGO 292 has 13 glutamic acid residues in theregion from the amino terminus of (both the immature and mature formsof) the protein and the tryptophan residue at amino acid residue 93 ofSEQ ID NO: 310, and also has another glutamic acid residue at position95 of SEQ ID NO: 310 which can also be carboxylated. In addition, humanTANGO 292 protein has four sets of paired (i.e., adjacent) glutamic acidresidues, at residues 33-34, 40-41, 71-72, and 77-78 and a pair ofglutamic acid residues (66 and 68) which are separated by a singleresidue. Similarly, gerbil TANGO 292 has 12 glutamic acid residues inthe region from the amino terminus of (both the immature and matureforms of) the protein and the tryptophan residue at amino acid residue92 of SEQ ID NO: 353, and also has another glutamic acid residue atposition 94 of SEQ ID NO: 353 which can also be carboxylated. Inaddition, gerbil TANGO 292 protein has three sets of glutamic acidresidues, at residues 70-71, 76-77, and 86-87, and a pair of glutamicacid residues (65 and 67) which are separated by a single residue. Theprotein of the invention includes proteins which are carboxylated at oneor more of the individual or paired glutamic acid residues.

[0632] TANGO 292, like other vitamin K-dependent carboxylationdomain-containing proteins, is involved in binding, uptake, and responseto metal cations such as calcium, to proteins, and to small molecules.Other proteins in which a vitamin K-dependent carboxylation domainoccurs include, for example, osteocalcin (bone-Gla protein), matrix Glaprotein, various plasma proteins such as prothrombin, coagulationfactors VII, IX, and X, proline rich Gla domain-containing proteins PRGP1 and PRGP2, and proteins C, S, and Z. Thus, TANGO 292 is involved inphysiological processes in which one or more of these other vitaminK-dependent carboxylation domain-containing proteins is involved.

[0633] The signal peptide prediction program SIGNALP (Nielsen et al.(1997) Protein Engineering 10:1-6) predicted that human TANGO 292protein includes an approximately 17 (i.e., 15, 16, 17, 18, or 19) aminoacid residue signal peptide (amino acid residues 1 to 17 of SEQ ID NO:310; SEQ ID NO: 311) preceding the mature TANGO 292 protein (i.e.,approximately amino acid residues 18 to 226 of SEQ ID NO: 310; SEQ IDNO: 312). In one embodiment, human TANGO 292 protein includes anextracellular domain (amino acid residues 18 to 113 of SEQ ID NO: 310;SEQ ID NO: 313); a transmembrane domain (amino acid residues 114 to 138of SEQ ID NO: 310; SEQ ID NO: 314); and a cytoplasmic domain (amino acidresidues 139 to 225 of SEQ ID NO: 310; SEQ ID NO: 315). In analternative embodiment, human TANGO 292 protein includes a cytoplasmicdomain (amino acid residues 18 to 113 of SEQ ID NO: 310; SEQ ID NO:313); a transmembrane domain (amino acid residues 114 to 138 of SEQ IDNO: 310; SEQ ID NO: 314); and an extracellular domain (amino acidresidues 139 to 225 of SEQ ID NO: 310; SEQ ID NO: 315).

[0634] The SignalP program predicted that gerbil TANGO 292 proteinincludes an approximately 17 (i.e., 15, 16, 17, 18, or 19) amino acidresidue amino acid signal peptide (amino acid residues 1 to 17 of SEQ IDNO: 353; SEQ ID NO: 354) preceding the mature TANGO 292 protein (i.e.,approximately amino acid residues 18 to 225 of SEQ ID NO: 353; SEQ IDNO: 355). In one embodiment, gerbil TANGO 292 protein includes anextracellular domain (amino acid residues 18 to 112 of SEQ ID NO: 353;SEQ ID NO: 356); a transmembrane domain (amino acid residues 113 to 137of SEQ ID NO: 353; SEQ ID NO: 357); and a cytoplasmic domain (amino acidresidues 138 to 225 of SEQ ID NO: 353; SEQ ID NO: 358). In analternative embodiment, gerbil TANGO 292 protein includes a cytoplasmicdomain (amino acid residues 18 to 112 of SEQ ID NO: 353; SEQ ID NO:356); a transmembrane domain (amino acid residues 113 to 137 of SEQ IDNO: 353; SEQ ID NO: 357); and an extracellular domain (amino acidresidues 138 to 225 of SEQ ID NO: 353; SEQ ID NO: 358).

[0635]FIG. 22D depicts a hydrophobicity plot of human TANGO 292 protein.

[0636] Relatively hydrophobic regions are above the dashed horizontalline, and relatively hydrophilic regions are below the dashed horizontalline. The hydrophobic region which corresponds to amino acid residues 1to 17 of SEQ ID NO: 310 is the signal sequence of human TANGO 292. Thehydrophobic region which corresponds to amino acid residues 114 to 138of SEQ ID NO: 310 is the transmembrane domain of human TANGO 292. Asdescribed elsewhere herein, relatively hydrophilic regions are generallylocated at or near the surface of a protein, and are more frequentlyeffective immunogenic epitopes than are relatively hydrophobic regions.For example, the region of human TANGO 292 protein from about amino acidresidue 90 to about amino acid residue 110 appears to be located at ornear the surface of the protein, while the region from about amino acidresidue 190 to about amino acid residue 195 appears not to be located ator near the surface.

[0637]FIG. 22M depicts a hydrophobicity plot of gerbil TANGO 292protein. Relatively hydrophobic regions are above the dashed horizontalline, and relatively hydrophilic regions are below the dashed horizontalline. The hydrophobic region which corresponds to amino acid residues 1to 17 of SEQ ID NO: 353 is the signal sequence of gerbil TANGO 292. Thehydrophobic region which corresponds to amino acid residues 113 to 137of SEQ ID NO: 353 is the transmembrane domain of gerbil TANGO 292. Asdescribed elsewhere herein, relatively hydrophilic regions are generallylocated at or near the surface of a protein, and are more frequentlyeffective immunogenic epitopes than are relatively hydrophobic regions.For example, the region of gerbil TANGO 292 protein from about aminoacid residue 90 to about amino acid residue 110 appears to be located ator near the surface of the protein.

[0638] An alignment of the human (H) and gerbil (G) ORF sequencesencoding TANGO 292 protein is shown in FIGS. 221-22K. This alignment wasmade using the ALIGN software {Myers and Miller (1989) CABIOS, ver.2.0}; pam120.mat scoring matrix; gap opening penalty=12, gap extensionpenalty=4), and indicates about 64.1% identity between these two cDNAsequences. An alignment of the amino acid sequences of gerbil (G) andhuman (H) TANGO 292 proteins is shown in FIG. 22L. In this alignment(made using the ALIGN software {Myers and Miller (1989) CABIOS, ver.2.0}; pam120.mat scoring matrix; gap opening penalty=12, gap extensionpenalty=4), the proteins are about 77.7% identical and about 80%similar.

[0639] The predicted molecular weight of human TANGO 292 protein withoutmodification and prior to cleavage of the signal sequence is about 25.4kilodaltons. The predicted molecular weight of the mature human TANGO292 protein without modification and after cleavage of the signalsequence is about 23.6 kilodaltons. The predicted molecular weight ofgerbil TANGO 292 protein without modification and prior to cleavage ofthe signal sequence is about 25.4 kilodaltons. The predicted molecularweight of the mature human TANGO 292 protein without modification andafter cleavage of the signal sequence is about 23.5 kilodaltons.

[0640] Northern analysis experiments indicated that human mRNAcorresponding to the cDNA encoding TANGO 292 is expressed in the tissueslisted in Table XXIc, wherein “++” indicates strong expression, “+”indicates lower expression, “+/−” indicates still lower expression, andindicates that expression could not be detected in the correspondingtissue. TABLE XXIc Animal Tissue Relative Level of Expression Humanplacenta ++ liver ++ kidney ++ lung + pancreas + heart +/− brain −skeletal muscle −

[0641] Uses of INTERCEPT 292 Nucleic Acids,

[0642] Polypeptides, and Modulators Thereof

[0643] TANGO 292 proteins are involved in disorders which affect bothtissues in which they are normally expressed and tissues in which theyare normally not expressed. Based on the observation that TANGO 292 isexpressed in human embryonic keratinocytes, and in placenta, liver,kidney, lung, pancreas, and heart tissues, TANGO 292 protein is involvedin one or more biological processes which occur in these tissues. Inparticular, TANGO 292 is involved in modulating growth, proliferation,survival, differentiation, and activity of cells including, but notlimited to, keratinocytes and cells with which keratinocytes interact inthe animal in which TANGO 292 is normally expressed. TANGO 292 is alsoinvolved in modulating growth, proliferation, survival, differentiation,and activity of placenta, liver, kidney, lung, pancreas, and heartcells. Thus, TANGO 292 has a role in disorders which affect these cellsand their growth, proliferation, survival, differentiation, andactivity. TANGO 292 polypeptides, nucleic acids, and modulators thereofcan be used to prognosticate, diagnose, inhibit, prevent, or alleviateone or more of these disorders.

[0644] In another example, TANGO 292 polypeptides, nucleic acids, andmodulators thereof can be used to treat placental disorders, such asthose described elsewhere in this disclosure. TANGO 292 polypeptides,nucleic acids, and modulators thereof can be used to prognosticate,diagnose, inhibit, prevent, or alleviate one or more of these disorders.

[0645] In another example, TANGO 292 polypeptides, nucleic acids, andmodulators thereof, can be used to treat hepatic (i.e., liver)disorders, such as the liver disorders described elsewhere in thisdisclosure. TANGO 292 polypeptides, nucleic acids, and modulatorsthereof can be used to prognosticate, diagnose, inhibit, prevent, oralleviate one or more of these disorders.

[0646] In another example, TANGO 292 polypeptides, nucleic acids, ormodulators thereof, can be used to treat renal (i.e., kidney) disorders,such as the kidney disorders described elsewhere in this disclosure.TANGO 292 polypeptides, nucleic acids, and modulators thereof can beused to prognosticate, diagnose, inhibit, prevent, or alleviate one ormore of these disorders.

[0647] TANGO 292 polypeptides, nucleic acids, and modulators thereof canbe associated with pulmonary (i.e., lung) disorders, such as the lungdisorders described elsewhere in this disclosure. TANGO 292polypeptides, nucleic acids, or modulators thereof can be used toprognosticate, diagnose, inhibit, prevent, or alleviate one or more ofthese disorders.

[0648] Pancreatic disorders in which TANGO 292 can be involved includethe pancreatic disorders described elsewhere in this disclosure. TANGO292 polypeptides, nucleic acids, or modulators thereof can be used toprognosticate, diagnose, inhibit, prevent, or alleviate one or more ofthese disorders.

[0649] Because TANGO 292 exhibits expression in the heart, TANGO 292nucleic acids, proteins, and modulators thereof can be used to treatcardiovascular disorders.

[0650] Examples of cardiovascular disorders with which TANGO 292 can beinvolved include those described elsewhere in this disclosure. TANGO 292polypeptides, nucleic acids, or modulators thereof can be used toprognosticate, diagnose, inhibit, prevent, or alleviate one or more ofthese disorders.

[0651] Presence in TANGO 292 of a vitamin K-dependent carboxylation(Gla) domain indicates that TANGO 292 is involved in physiologicalfunctions identical or analogous to the functions performed by otherproteins having such domains. For example, like other Gladomain-containing proteins, TANGO 292 modulates binding and uptake ofcalcium and other metal ions by cells which express it and the responseof those cells to the presence and uptake of such ions. Human matrix Glaprotein, for example, is involved in Keutel syndrome, an autosomalrecessive disorder characterized by abnormal cartilage calcification,peripheral pulmonary stenosis, and midfacial hypoplasia (Munroe et al.(1999) Nat. Genet. 21:142-144). Other proteins containing a Gla domaininclude, for example, two human proline-rich Gla proteins designatedPRGPI and PRGP2, human G domain-containing protein Gas6, and severalhuman blood coagulation factors (Kulman et al. (1997) Proc. Natl. Acad.Sci. USA 94:9058-9062; Mark et al., (1996) J. Biol. Chem. 271:9785-9786;Cancela et al. (1990) J. Biol. Chem. 265:15040-15048). These proteinsare involved in binding of mineral ions such as calcium, phosphate, andhydroxyapatite, binding of proteins, binding of vitamins and smallmolecules, and mediation of blood coagulation. Thus, TANGO 292 isinvolved in numerous physiological processes which are influenced bylevels of calcium and other metal ions in body fluids or by the presenceof proteins, vitamins, or small molecules. Such processes include, forexample, bone uptake, maintenance, and deposition, formation,maintenance, and repair of cartilage, formation and maintenance ofextracellular matrices, movement of cells through extracellularmatrices, coagulation and dissolution of blood components (e.g., bloodcells and proteins), and deposition of materials (e.g., lipids, cells,calcium, and the like) in arterial walls. TANGO 292 polypeptides,nucleic acids, and modulators thereof can be used to prognosticate,diagnose, inhibit, prevent, or alleviate one or more of these disorders.

[0652] TANGO 292 is involved in disorders which affect the tissues inwhich it is normally expressed and upon which it normally acts. Thus,TANGO 292 is involved in disorders which involve aberrant binding oraberrant failure to bind of keratinocytes or similar cells with a tissueaffected by the disorder. Such disorders include, by way of example andnot limitation, osteoporosis, (repair of) traumatic bone injuries,rickets, osteomalacia, Paget's disease, and other bone disorders,osteoarthritis, rheumatoid arthritis, ankylosing spondylitis, Keutelsyndrome, and other disorders of the joints and cartilage, irondeficiency anemia, hemophilia, inappropriate blood coagulation, stroke,arteriosclerosis, atherosclerosis, aneurysm, and other disorders relatedto blood and blood vessels, metastasis and other disorders related toinappropriate movement of cells through extracellular matrices, and thelike. TANGO 292 polypeptides, nucleic acids, and modulators thereof canbe used to prognosticate, diagnose, inhibit, prevent, or alleviate oneor more of these disorders.

[0653] TANGO 331

[0654] A cDNA clone (designated jthvb042g08) encoding at least a portionof human TANGO 331 protein was isolated from a human mammary epitheliumcDNA library. A corresponding cDNA clone (designated jchrc045a03) wasisolated from a human heart library. The human TANGO 331 protein ispredicted by structural analysis to be a secreted protein.

[0655] The full length of the cDNA encoding human TANGO 331 protein(FIG. 23; SEQ ID NO: 324) is 1432 nucleotide residues. The ORF of thiscDNA, nucleotide residues 114 to 1172 of SEQ ID NO: 324 (i.e., SEQ IDNO: 325), encodes a 353-amino acid secreted protein (FIG. 23; SEQ ID NO:326).

[0656] The invention thus includes purified human TANGO 331 protein,both in the form of the immature 353 amino acid residue protein (SEQ IDNO: 326) and in the form of the mature, approximately 329 amino acidresidue protein (SEQ ID NO: 328). Mature human TANGO 331 protein can besynthesized without the signal sequence polypeptide at the aminoterminus thereof, or it can be synthesized by generating immature TANGO331 protein and cleaving the signal sequence therefrom.

[0657] The invention includes nucleic acid molecules which encode aTANGO 331 polypeptide of the invention. Such nucleic acids include, forexample, a DNA molecule having the nucleotide sequence listed in SEQ IDNO: 324 or some portion thereof, such as the portion which encodesmature TANGO 331 protein, immature TANGO 331 protein, or a domain ofTANGO 331 protein. These nucleic acids are collectively referred to asTANGO 331 nucleic acids of the invention.

[0658] TANGO 331 proteins and nucleic acid molecules encoding themcomprise a family of molecules having certain conserved structural andfunctional features, as indicated by the conservation of amino acidsequence between human TANGO 331 protein and the Chinese hamster(Cricetulus griseus) protein designated HT and having GenBank Accessionnumber U48852, as shown in FIG. 23E, and the conservation of nucleotidesequence between the ORFs encoding human TANGO 331 protein and Chinesehamster protein HT, as shown in FIGS. 23F through 23J.

[0659] A common domain present in TANGO 331 proteins is a signalsequence. In one embodiment, a TANGO 331 protein contains a signalsequence corresponding to about amino acid residues 1 to 24 of SEQ IDNO: 326 (SEQ ID NO: 327). The signal sequence is cleaved duringprocessing of the mature protein.

[0660] TANGO 331 proteins can include an extracellular domain. The humanTANGO 331 protein is a secreted protein, and thus includes an‘extracellular domain’ consisting of the entire mature protein (i.e.,approximately residues 25 to 353 of SEQ ID NO: 326; SEQ ID NO: 328).

[0661] TANGO 331 proteins typically comprise a variety of potentialpost-translational modification sites (often within an extracellulardomain), such as those described herein in Table XXII, as predicted bycomputerized sequence analysis of TANGO 331 proteins using amino acidsequence comparison software (comparing the amino acid sequence of TANGO331 with the information in the PROSITE database {rel. 12.2; February1995} and the Hidden Markov Models database {Rel. PFAM 3.3}). In certainembodiments, a protein of the invention has at least 1, 2, 4, 6, 10, 15,or 20 or more of the post-translational modification sites listed inTable XXII. TABLE XXII Amino Acid Type of Potential Modification SiteResidues of Amino Acid or Domain SEQ ID NO: 326 Sequence N-glycosylationsite 190 to 193 NETH 251 to 254 NGSY cAMP-or cGMP-dependent protein 26to 29 KKPT kinase phosphorylation site Protein kinase C phosphorylationsite 48 to 50 TAK 123 to 125 TLK 144 to 146 SQR 165 to 167 SCR 187 to189 SLR 202 to 204 SCK 210 to 212 TNR Casein kinase II phosphorylationsite 58 to 61 TAWE 66 to 69 SKYE 86 to 89 SDFE 197 to 200 TACD 210 to213 TNRD 255 to 258 TCEE 295 to 298 SLAE 339 to 342 TEGE 349 to 352 SREDTyrosine kinase phosphorylation site 303 to 309 RKNENCY N-myristoylationsite 44 to 49 GMVDTA 54 to 59 GGGNTA 81 to 86 GLCESS 150 to 155 GNGHCS158 to 163 GSRQGD 164 to 169 GSCRCH 252 to 257 GSYTCE 313 to 318 GSYVCVAspartic acid and asparagine 308 to 319 See FIG. 23 hydroxylation siteEGF-like domain cysteine pattern 166 to 177 See FIG. 23 signature EGFdomain 140 to 177 See FIG. 23 234 to 263 See FIG. 23 301 to 330 See FIG.23 Laminin-like EGF domain 153 to 199 See FIG. 23 TNFR/NGFRcysteine-rich region 180 to 214 See FIG. 23 domain Vertebratemetallothionein-like domain 229 to 298 See FIG. 23 Leucine Zipper domain 94 to 115 See FIG. 23

[0662] Among the domains that occur in TANGO 331 protein are EGFdomains, including a laminin-like EGF domain, a TNFR/NGFR cysteine-richdomain, a metallothionein-like domain, and a leucine zipper domain.

[0663] EGF-like domains are about 30 to 40 amino acid residues in lengthand comprise several conserved cysteine residues in one of severalpatterns. EGF-like domains occur in a large number of proteinsincluding, for example, human epidermal growth factor (EGF), murineadipocyte differentiation inhibitor, human agrin, human growth factoramphiregulin, human growth factor betacellulin, sea urchin blastulatissue patterning proteins BP10 and Span, cattle tick glycoprotein BM86,human bone morphogenic protein 1, sea urchin suBMP, Drosophila tolloidprotein, Caenorhabditis elegans developmental proteins lin-12 and glp-1,C. elegans tissue patterning protein APX-I, human calcium-dependentserine proteinase, human cartilage matrix protein, human cartilageoligomeric matrix protein, human cell surface antigen 114 μl 0, rat cellsurface glycoprotein complex transmembrane subunit ASGP-2, humancoagulation associated proteins C, Z, and S, human coagulation factorsVII, IX, X, and XII, human complement components Clr, Cls, C6, C7, C8α,C8β, and C9, human complement-activating components of Ra-reactivefactor, Drosophila epithelial development protein Crumbs, sea urchinexogastrula-inducing peptides A, C, D, and X, Drosophilacadherin-related tumor suppressor protein Fat, human fetal antigen I (aneuroendocrine differentiation protein derived from the delta-likeprotein), human fibrillins 1 and 2, sea urchin fibropellins IA, IB, IC,II, and III, human extracellular matrix proteins fibulin-1 and -2,Drosophila cell determination/axon guidance protein Argos, variouspoxvirus growth factor-related proteins, Drosophila developmentalprotein Gurken, human heparin-binding EGF-like growth factor, humantransforming growth factor-α, human growth factors Lin-3 and Spitz,human hepatocyte growth factor activator, human LDL and VLDL receptors,human LDL receptor-related protein, human leukocyte antigen CD97, humancell surface glycoprotein EMRI, human cell surface glycoprotein F4/80,Japanese horseshoe crab limulus clotting factor C, mammalianmembrane-bound endopeptidase Meprin A a subunit, murine milk fatglobule-EGF factor 8, human glial growth factors neuregulin GGF-I andGGF-II, mammalian neurexins, human neurogenic proteins Notch, Xotch,Tan-], and Delta, C. elegans differentiation protein Lag-2, Drosophiladifferentiation proteins Serrate and Slit, chordate basement membraneprotein Nidogen, Plasmodium ookinete 24, 25, and 28 kilodalton surfaceproteins, human pancreatic secretory granule membrane glycoprotein GP2,human non-specific cell lysis protein Perforin, human proteoglycansaggrecan, versican, perlecan, brevican, and chondroitin sulfate, humanendoplasmic reticulum prostaglandin G/H synthases 1 and 2, humanextracellular protein S1-5, human autocrine growth factorSchwannoma-derived growth factor, human E-, P—, and L-selectins,Arabidopsis thaliana chlorophyll complex assembly proteinserine/threonine-protein kinase homolog, guinea pig sperm-egg fusionproteins PH-30a and 1, murine stromal cell derived protein-I, humanteratocarcinoma-derived growth factor, mammalian extracellular proteintenascin, chicken extracellular protein TEN-A, human tenascin-X,Drosophila tenascin-like proteins TEN-A and TEN-M, human protein Cactivator thrombomodulin, human adhesive glycoproteins thrombospondins1, 2, 3, and 4, human thyroid peroxidases 1 and 2, human transforminggrowth factor β1-1 binding protein, human tyrosine-protein kinasereceptors Tek and Tie, human urokinase-type plasminogen activator, humantissue plasminogen activator, human uromodulin, human vitaminK-dependent anticoagulant proteins C and S (and the related humansingle-chain plasma glycoprotein Z), the sea urchin 63 kilodalton spermflagellar membrane protein, chicken Nel protein, and the hypothetical C.Elegans protein T20G5.3. Although these proteins have a variety ofactivities and sites of expression, a common characteristic of most ofthem is that they are involved in protein-to-protein binding in theextracellular space—either to a secreted protein, a component of theextracellular matrix, or to an extracellular portion of an integralmembrane protein. Based on this shared characteristic, the presence ofmultiple EGF-like domains in TANGO 331 indicates that TANGO 331 isinvolved in binding to proteins extracellularly.

[0664] Post-translational hydroxylation of aspartic acid or asparagineto form erythro-β-hydroxyaspartic acid or erythro-β-hydroxyasparagineoccurs in various proteins having one or more EGF-like domains (e.g.,blood coagulation protein factors VII, IX, and X, blood coagulationproteins C, S, and Z, the LDL receptor, thrombomodulin, and the like).TANGO 331 has a signature sequence which is characteristic ofhydroxylation of the asparagine residue at amino acid residue 310. Theinvention thus includes TANGO 331 proteins having a hydroxylatedasparagine residue at position 310 of SEQ ID NO: 326.

[0665] TNFR/NGFR (tumor necrosis factor receptor/nerve growth factorreceptor) cysteine-rich region domains are about 30 to 40 amino acidresidues in length, and generally exhibit a conserved pattern of six ormore cysteine residues. These domains occur in several soluble andtransmembrane proteins which are known to be receptors for growthfactors or for cytokines. Examples of TNFR/NGFR cysteine-rich regiondomain-containing proteins are human tumor necrosis factor (TNF)cysteine-rich region domains type I and type II receptors, Shope fibromavirus soluble TNF receptor, human lymphotoxin α/β, human low-affinitynerve growth factor receptor, human CD40L (cytokine) receptor CD40,human CD27L (cytokine) receptor CD27, human CD30L (cytokine) receptorCD30, human T-cell cytokine receptor 4-1BB, human apoptotic FASL proteinreceptor FAS, human T-cell OX40L (cytokine) receptor OX40, humanapoptosis-related receptor Wsl-1, and Vaccinia protein A53. Presence ofa TNFR/NGFR cysteine-rich region domain in TANGO 331 is an indicationthat TANGO 331 is involved in one or more physiological processesinvolving extracellular binding with a cytokine or growth factor. Suchprocesses include, for example, growth, homeostasis, regeneration, andproliferation of cells and tissues, immune (including autoimmune)responses, host defenses against infection, and the like.

[0666] Metallothioneins are cysteine-rich proteins which are capable ofbinding heavy metals such as calcium, zinc, copper, cadmium, cobalt,nickel, and the like. Proteins which have a domain which resembles ametal-binding domain of a metallothionein are also capable of bindingsuch metals. TANGO 331 comprises a metallothionein-like domain, and iscapable of binding one or more heavy metals. This is an indication thatTANGO 331 is involved in one or more physiological processes whichinvolve metal binding. Such processes include, by way of example and notlimitation, nutritional supply of metals to cells on a controlled basis,removal of toxic metal species from body tissues, storage of metals, andthe like.

[0667] TANGO 331 comprises a leucine zipper region at about amino acidresidue 94 to about amino acid residue 115 (i.e., 94LeaqeehLeawwlqLkseypdL 115; SEQ ID NO: 460). Leucine zipper regions areknown to be involved in dimerization of proteins. Leucine zipper regionsinteract with one another, leading to formation of homo- orhetero-dimers between proteins, depending on their identity. Thepresence in TANGO 331 of a leucine zipper region is a further indicationthat this protein is involved in protein-protein interactions.

[0668] TANGO 331 shares amino acid and nucleic acid homology with aChinese hamster protein designated HT, and thus is involved incorresponding physiological processes in humans. An alignment of theamino acid sequences of (human) TANGO 331 and Chinese hamster protein HTis shown in FIG. 23E. In this alignment (made using the ALIGN software{Myers and Miller (1989) CABIOS, ver. 2.0}; pam120.mat scoring matrix;gap opening penalty=12, gap extension penalty=4), the proteins are 71.9%identical. An alignment of the nucleotide sequences of the ORFs encoding(human) TANGO 331 and Chinese hamster protein HT is shown in FIGS. 23Fthrough 23J. The two ORFs are 74.5% identical, as assessed using thesame software and parameters.

[0669] The signal peptide prediction program SIGNALP (Nielsen et al.(1997) Protein Engineering 10:1-6) predicted that human TANGO 331protein includes an approximately 24 (i.e., 22, 23, 24, 25, or 26) aminoacid residue signal peptide (amino acid residues 1 to 24 of SEQ ID NO:326; SEQ ID NO: 327) preceding the mature TANGO 331 protein (i.e.,approximately amino acid residues 25 to 353 of SEQ ID NO: 326; SEQ IDNO: 328). Mature human TANGO 331 is a secreted protein.

[0670]FIG. 23D depicts a hydrophobicity plot of human TANGO 331 protein.Relatively hydrophobic regions are above the dashed horizontal line, andrelatively hydrophilic regions are below the dashed horizontal line. Thehydrophobic region which corresponds to amino acid residues 1 to 24 ofSEQ ID NO: 326 is the signal sequence of human TANGO 331 (SEQ ID NO:327). As described elsewhere herein, relatively hydrophilic regions aregenerally located at or near the surface of a protein, and are morefrequently effective immunogenic epitopes than are relativelyhydrophobic regions. For example, the region of human TANGO 331 proteinfrom about amino acid residue 140 to about amino acid residue 170appears to be located at or near the surface of the protein, while theregion from about amino acid residue 115 to about amino acid residue 130appears not to be located at or near the surface.

[0671] The predicted molecular weight of human TANGO 331 protein withoutmodification and prior to cleavage of the signal sequence is about 38.2kilodaltons. The predicted molecular weight of the mature human TANGO331 protein without modification and after cleavage of the signalsequence is about 35.6 kilodaltons.

[0672] Tissue distribution of TANGO 331 mRNA was determined by Northernblot hybridization. Northern blot hybridizations with the various RNAsamples were performed using standard Northern blotting conditions andwashing under stringent conditions (i.e., 0.2×SSC at 65° C.). The DNAprobe used in the Northern Blot experiments was radioactively labeledwith ³²P-dCTP using the PRIME-IT™ kit (Stratagene, La Jolla, Calif.)according to the instructions of the supplier. Filters having human mRNAdisposed thereon (MULTITISSUE™ Northern I and MULTITISSUE™ Northern IIobtained from Clontech, Palo Alto, Calif.) were probed in EXPRESSHYB™hybridization solution (Clontech) and washed at high stringencyaccording to the manufacturer's recommendations.

[0673] Two isoforms of human TANGO 331 were identified using thisNorthern blot analysis, indicating that TANGO 331 can have a splicevariant. One isoform (corresponding to the larger message) can be atransmembrane protein (frizzled-like) and the other (i.e., smaller)isoform can be a secreted form. The two isoforms exhibit a clear patternof tissue specificity. On the multiple tissue blot from Clonetech, thelarge transcript is found in almost all tissues, whereas the smallermessage is expressed mainly in heart, skeletal muscle, placenta, andpancreas tissues.

[0674] TANGO 331 can be expressed as a recombinantglutathione-S-transferase (GST) fusion polypeptide in E. coli and thefusion polypeptide is isolated and characterized. Specifically, TANGO331 can be fused with GST and this fusion polypeptide can expressed inE. coli, e.g., in strain PEBI99. Expression of the GST-TANGO 331 fusionprotein in PEB199 is induced with IPTG. The recombinant fusionpolypeptide can be purified from crude bacterial lysates of the inducedPEB199 strain by affinity chromatography, e.g., usingglutathione-substituted beads. Using polyacrylamide gel electrophoreticanalysis of the polypeptide purified from the bacterial lysates, themolecular weight of the resultant fusion polypeptide can be determined.

[0675] To express the TANGO 331 gene in COS cells, the pcDNA/Amp vectorby Invitrogen Corporation (San Diego, Calif.) can be used. This vectorcontains an SV40 origin of replication, an ampicillin resistance gene,an E. coli replication origin, a CMV promoter followed by a polylinkerregion, and an SV40 intron and polyadenylation site. A DNA fragmentencoding the entire TANGO 331 protein and an HA tag (Wilson et al.(1984) Cell 37:767) or a FLAG tag fused in-frame to its 3′ end of thefragment can be cloned into the polylinker region of the vector, therebyplacing the expression of the recombinant protein under the control ofthe CMV promoter.

[0676] To construct the plasmid, the TANGO 331 DNA sequence is amplifiedby PCR using two primers. The 5′ primer contains the restriction site ofinterest followed by approximately twenty nucleotides of the TANGO 331coding sequence starting from the initiation codon; the 3′ end sequencecontains complementary sequences to the other restriction site ofinterest, a translation stop codon, the HA tag or FLAG tag and the last20 nucleotides of the TANGO 331 coding sequence. The PCR amplifiedfragment and the pcDNA/Amp vector are digested with the appropriaterestriction enzymes and the vector is dephosphorylated using the CIAPenzyme (New England Biolabs, Beverly, Mass.). Preferably the tworestriction sites chosen are different so that the TANGO 331 gene isinserted in the correct orientation. The ligation mixture is transformedinto E. coli cells (e.g., one or more of strains HB101, DH5a, SURE,available from Stratagene Cloning Systems, La Jolla, Calif.), thetransformed culture is plated on ampicillin media plates, and resistantcolonies are selected. Plasmid DNA is isolated from transformants andexamined by restriction analysis for the presence of the correctfragment.

[0677] COS cells are subsequently transfected using the TANGO331-pcDNA/Amp plasmid DNA using the calcium phosphate or calciumchloride co-precipitation methods, DEAE-dextran-mediated transfection,lipofection, or electroporation. Other suitable methods of transfectinghost cells can be found in Sambrook, J., Fritsh, E. F., and Maniatis, T.Molecular Cloning: A Laboratory Manual. 2nd, ed., Cold Spring HarborLaboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor,N.Y., 1989. The expression of the TANGO 331 polypeptide can be detectedby radiolabelling (³⁵S-methionine or ³⁵S-cysteine available from NEN,Boston, Mass., can be used) and immunoprecipitation (Harlow, E. andLane, D. Antibodies: A Laboratory Manual, Cold Spring Harbor LaboratoryPress, Cold Spring Harbor, N.Y., 1988) using an HA specific monoclonalantibody. Briefly, the cells are labeled for 8 hours with ³⁵S-methionine(or ³⁵S-cysteine). The culture media are then collected and the cellsare lysed using detergents (RIPA buffer, 150 millimolar NaCl, 1% NP-40,0.1% SDS, 0.5% DOC, 50 millimolar Tris, pH 7.5). Both the cell lysateand the culture media are precipitated with an HA specific monoclonalantibody. Precipitated polypeptides are then analyzed by SDS-PAGE.

[0678] Alternatively, DNA containing the TANGO 331 coding sequence canbe cloned directly into the polylinker of the pCDNA/Amp vector using theappropriate restriction sites. The resulting plasmid is transfected intoCOS cells in the manner described above, and the expression of the TANGO331 polypeptide can be detected by radiolabelling andimmunoprecipitation using an TANGO 331 specific monoclonal antibody.

[0679] The human TANGO 331 gene was mapped using the Genebridge 4 HumanRadiation hybrid mapping panel with ATTATTCAGAAGGATGTCCCGTGG (SEQ ID NO:369) as the forward primer and CCTCCTGATTACCTACAATGGTC (SEQ ID NO: 370)as the reverse primer. The human TANGO 331 gene maps to human 22q11-q13.Flanking markers for this region are WI-4572 and WI-8917. Theschizophrenia 4 (sczd4) locus also maps to this region of the humanchromosome. Also mapping to this region of the human chromosome are thefollowing genes: transcription factor 20 (tcf20), Benzodiazepinereceptor, peripheral type (bzrp), Arylsulfatase A (arsa), diaphorase(NADH); cytochrome b-5 reductase (dial), and Solute carrier family 5(sodium/glucose transporter), member 1 (slcal). This region is syntenicto mouse chromosome 15. The stargazer (stg), gray tremor (gt), brachyurymodifier 2 (Brm2), bronchial hyperresponsiveness 2 (Bhr2), loss ofrighting induced by ethanol 5 (Lore5), fluctuating asymmetry QTL 8(Faq8), jerky (Jrk), belted (bt), and koala (Koa) loci also map to thisregion of the mouse chromosome, several of which are neuromuscularrelated.

[0680] Uses of TANGO 331 Nucleic Acids,

[0681] Polypeptides, and Modulators Thereof

[0682] TANGO 331 proteins are involved in disorders which affect bothtissues in which they are normally expressed and tissues in which theyare normally not expressed. Based on the observation that TANGO 331 isexpressed in human mammary epithelial tissue and human heart tissue,TANGO 331 protein is involved in one or more biological processes whichoccur in mammary epithelial tissue, in other epithelial tissues, and inheart tissue. In particular, TANGO 331 is involved in modulating growth,proliferation, survival, differentiation, and activity of cellsincluding, but not limited to, epithelial cells (e.g., mammaryepithelial cells) of the animal in which it is normally expressed. Thus,TANGO 331 has a role in disorders which affect these cells and theirgrowth, proliferation, survival, differentiation, and activity. TANGO331 is therefore involved in physiological processes such as maintenanceof epithelia, carcinogenesis, modulation and storage of protein factorsand metals, and lactation. Furthermore, because TANGO 331 is expressedin human mammary epithelial cells, it also has a role in nutrition ofhuman infants (e.g., providing nutrients such as minerals to infants andproviding protein factors not synthesized by infants) and in disorderswhich affect them. Thus, TANGO 331 is involved in a number of disorderssuch as breast cancer, insufficient lactation, infant nutritional andgrowth disorders, and the like. TANGO 331 polypeptides, nucleic acids,or modulators thereof can be used to prognosticate, diagnose, inhibit,prevent, or alleviate one or more of these disorders.

[0683] Because TANGO 331 exhibits expression in the heart, TANGO 331nucleic acids, proteins, and modulators thereof can be used to treatcardiovascular disorders. Examples of cardiovascular disorders withwhich TANGO 331 can be involved include those described elsewhere inthis disclosure. TANGO 331 polypeptides, nucleic acids, or modulatorsthereof can be used to prognosticate, diagnose, inhibit, prevent, oralleviate one or more of these disorders.

[0684] In another example, TANGO 331 polypeptides, nucleic acids, andmodulators thereof, can be involved in normal and aberrant functioningof skeletal muscle tissue, and can thus be involved in disorders of suchtissue. Examples of skeletal muscle disorders are described elsewhere inthis disclosure. TANGO 331 polypeptides, nucleic acids, or modulatorsthereof can be used to prognosticate, diagnose, inhibit, prevent, oralleviate one or more of these disorders.

[0685] In another example, TANGO 331 polypeptides, nucleic acids, andmodulators thereof can be used to treat placental disorders, such asthose described elsewhere in this disclosure. TANGO 331 polypeptides,nucleic acids, or modulators thereof can be used to prognosticate,diagnose, inhibit, prevent, or alleviate one or more of these disorders.

[0686] Presence in TANGO 331 of numerous EGF-like domains, including thelaminin-like EGF-like domain indicates that TANGO 331 is involved inextracellular binding of proteins, including both other secretedproteins (e.g., growth factors and cytokines) and cell-surface proteins.Binding of TANGO 331 to other secreted proteins modulates theiractivity, their rate of uptake by cells, and their rate of degradation.Binding of TANGO 331 to cell surface proteins modulates their activity,including, for example, their ability to bind with other secretedproteins, and transmits a signal to the cell expressing the cell-surfaceprotein. Presence in TANGO 331 of a TNFR/NGFR cysteine-rich regiondomain is further indicative of the ability of TANGO 331 to bind withgrowth factors and cytokines. Thus, TANGO 331 is involved in a number ofproliferative and immune disorders including, but not limited to,cancers (e.g., breast cancer), autoimmune disorders, insufficient orinappropriate host responses to infection, acquired immune deficiencysyndrome, and the like. TANGO 331 polypeptides, nucleic acids, ormodulators thereof can be used to prognosticate, diagnose, inhibit,prevent, or alleviate one or more of these disorders.

[0687] The fact that TANGO 331 has a metallothionein-like region isindicative of the ability of TANGO 331 to bind with metal ions,including nutritionally required metal ions (e.g., calcium, magnesium,zinc, manganese, cobalt, iron, and the like). Thus, TANGO 331 isinvolved in binding with essential minerals and in delivering them totheir proper body locations. TANGO 331 is also involved in bindingexcess or toxic metal ions so that they can be excreted. TANGO 331 isthus involved in disorders involving insufficient or inappropriatelocalization of metal ions. Such disorders include, but are not limitedto, malnutrition and mineral deficiency disorders, hemochromatosis,inappropriate calcification of body tissues, bone disorders such asosteoporosis, and the like. TANGO 331 polypeptides, nucleic acids, ormodulators thereof can be used to prognosticate, diagnose, inhibit,prevent, or alleviate one or more of these disorders.

[0688] Mapping of the human TANGO 331 gene to chromosomal region22q11-q13 is an indication of disorders with which its expression (ornon- or aberrant-expression) can be associated. For example,arylsulfatase A is associated with Metachromatic leukodystrophy.Diaphorase (NADH:cytochrome b-5 reductase) is associated withmethemoglobinemia, types I and II. Solute carrier family 5(sodium/glucose transporter), member 1 is associated withglucose/galactose malabsorption. The gene designated schizophrenia 4 isassociated with schizophrenia and velocardiofacial syndrome, asdescribed in Online Mendelian Inheritance in Man, Johns HopkinsUniversity, Baltimore, Md. MIM Number: 600850:12/7/98. (World Wide WebURL: http://www.ncbi.nlm.nih.gov/omim/). These mapping data indicatethat TANGO 331 polypeptides, nucleic acids, and modulators thereof canbe used to prognosticate, diagnose, inhibit, prevent, or alleviate oneor more of these disorders.

[0689] TANGO 332

[0690] A cDNA clone (designated jlhbab463g12) encoding at least aportion of human TANGO 332 protein was isolated from a human adult braincDNA library. The human TANGO 332 protein is predicted by structuralanalysis to be a secreted protein.

[0691] The full length of the cDNA encoding human TANGO 332 protein(FIG. 24; SEQ ID NO: 329) is 2730 nucleotide residues. The ORF of thiscDNA, nucleotide residues 173 to 2185 of SEQ ID NO: 329 (i.e., SEQ IDNO: 330), encodes a 671-amino acid transmembrane protein (FIG. 24; SEQID NO: 331).

[0692] The invention thus includes purified human TANGO 332 protein,both in the form of the immature 671 amino acid residue protein (SEQ IDNO: 331) and in the form of the mature, approximately 649 amino acidresidue protein (SEQ ID NO: 333). Mature human TANGO 332 protein can besynthesized without the signal sequence polypeptide at the aminoterminus thereof, or it can be synthesized by generating immature TANGO332 protein and cleaving the signal sequence therefrom.

[0693] The invention includes nucleic acid molecules which encode aTANGO 332 polypeptide of the invention. Such nucleic acids include, forexample, a DNA molecule having the nucleotide sequence listed in SEQ IDNO: 329 or some portion thereof, such as the portion which encodesmature TANGO 332 protein, immature TANGO 332 protein, or a domain ofTANGO 332 protein. These nucleic acids are collectively referred to asTANGO 332 nucleic acids of the invention.

[0694] TANGO 332 proteins and nucleic acid molecules encoding themcomprise a family of molecules having certain conserved structural andfunctional features, as indicated by the conservation of amino acidsequence between human TANGO 332 protein, human brain-enrichedhyaluronan-binding factor (BEF), as shown in FIGS. 24G and 24H, andmurine brevican protein, as shown in FIGS. 241 to 24K. This conservationis further indicated by conservation of nucleotide sequence between theORFs encoding human TANGO 332 protein and murine brevican protein, asshown in FIGS. 24L through 24U.

[0695] A common domain present in TANGO 332 proteins is a signalsequence. In one embodiment, a TANGO 332 protein contains a signalsequence corresponding to about amino acid residues 1 to 22 of SEQ IDNO: 331 (SEQ ID NO: 332). The signal sequence is cleaved duringprocessing of the mature protein.

[0696] TANGO 332 proteins are secreted proteins. The mature form ofhuman TANGO 332 protein has the amino acid sequence of approximatelyamino acid residues 23 to 671 of SEQ ID NO: 331.

[0697] TANGO 332 proteins typically comprise a variety of potentialpost-translational modification sites (often within an extracellulardomain), such as those described herein in Table XXIII, as predicted bycomputerized sequence analysis of TANGO 332 proteins using amino acidsequence comparison software (comparing the amino acid sequence of TANGO332 with the information in the PROSITE database {rel. 12.2; February1995} and the Hidden Markov Models database {Rel. PFAM 3.3}). In certainembodiments, a protein of the invention has at least 1, 2, 4, 6, 10, 15,or 20 or more of the post-translational modification sites listed inTable XXII. TABLE XXIII Amino Acid Type of Potential Modification SiteResidues of Amino Acid or Domain SEQ ID NO: 331 Sequence N-glycosylationsite 130 to 133 NDSG 337 to 340 NQTG Protein kinase C phosphorylationsite 67 to 69 SRR 74 to 76 SPR 165 to 167 SAR 212 to 214 TVR 219 to 221TPR 310 to 312 SVR 319 to 321 SQR 545 to 547 TPR 615 to 617 SGR Caseinkinase II phosphorylation site 29 to 32 SSED 116 to 119 SLTD 219 to 222TPRE 269 to 272 TLEE 382 to 385 TVTE 386 to 389 TLEE 397 to 400 TESE 419to 422 STPE 430 to 433 TLLE 446 to 449 SEEE 545 to 548 TPRE 558 to 561TLVE Tyrosine kinase phosphorylation site 128 to 135 RPNDSGIY 451 to 459KALEEEEKY N-myristoylation site 47 to 52 GVLGGA 133 to 138 GIYRCE 142 to147 GIDDSS 174 to 179 GAQEAC 183 to 188 GAHIAT 281 to 286 GAEIAT 288 to293 GQLYAA 297 to 302 GLDHCS 324 to 329 GGLPGV 403 to 408 GAIYSI 414 to419 GGGGSS 576 to 581 GVPRGE 586 to 591 GSSEGA Immunoglobulin-/major  50to 141 See FIG. 24 histocompatibility protein-like (Ig-/MHC-like) domainExtracellular link domain 156 to 251 See FIG. 24 257 to 353 See FIG. 24

[0698] Among the domains that occur in TANGO 332 protein are anIg-/MHC-like domain and a pair of extracellular link domains. In oneembodiment, the protein of the invention has at least one domain that isat least 55%, preferably at least about 65%, more preferably at leastabout 75%, yet more preferably at least about 85%, and most preferablyat least about 95% identical to one of these domains. In otherembodiments, the protein has at least one Ig-/MHC-like domain and oneextracellular link domain described herein in Table XXIII. In otherembodiments, the protein has at least one Ig-/MHC-like domain and atleast two extracellular link domains.

[0699] Ig-/MHC-like domains are conserved among immunoglobulin (1 g)constant (CL) regions and one of the three extracellular domains ofmajor histocompatibility proteins (MHC). The presence in TANGO 332 of anIg-/MHC-like domain indicates that the corresponding region of TANGO 332is structurally similar to this conserved extracellular region.

[0700] Extracellular link domains occur in hyaluronan-(HA-) bindingproteins. Proteins having this domain include cartilage link protein,proteoglycans such as aggrecan, brevican, neurocan, and versican, CD44antigen (the primary cell surface receptor for HA), and tumor necrosisfactor-inducible protein TSG-6. Presence of a pair of extracellular linkdomains in TANGO 332 indicates that this protein is also involved inHA-binding, and therefore is involved in physiological processes such ascartilage (and other tissue) organization, extracellular matrixorganization, neural growth and branching, and cell-to-cell andcell-to-matrix interactions. Involvement of TANGO 332 in these processesimplicates this protein in disorders such as tumor growth andmetastasis, movement of cells (e.g., leukocytes) through extracellularmatrix, inappropriate inflammation, and the like.

[0701] Brevican is a murine nervous system-specific chondroitin sulfateproteoglycan which binds in a calcium-dependent manner with two classesof sulfated glycolipids, namely sulfatides and HNK-1-reactivesulfoglucuronylglycolipids (Miura et al. (1999) J. Biol. Chem.274:11431-11438). A human orthologue, designated BEF (‘Brain-Enrichedhyaluronan-binding Factor’), of murine brevican is expressed by humanglioma cells, but not by brain tumors of non-glial origin (P.C.T.application publication number W098/31800; Zhang et al. (1998) J.Neurosci. 18:2370-2376). Those authors suggested that cleavage of thathuman orthologue mediates glioma cell invasion in vivo.

[0702] An alignment of the amino acid sequences of TANGO 332 and BEFprotein is shown in FIGS. 24G and 24H. In this alignment (made using theALIGN software {Myers and Miller (1989) CABIOS, ver. 2.0}; pam120.matscoring matrix; gap opening penalty=12, gap extension penalty=4), theproteins are 75.7% identical, although it is seen that TANGO 332includes two domains (one from about amino acid residue 152 to aboutresidue 208, and the other near the carboxyl terminus of TANGO 332)which do not occur in BEF protein. It is likely that these two regionsaccount for the differences between the physiological roles of TANGO 332and BEF.

[0703] An alignment of the amino acid sequences of (human) TANGO 332 andmurine brevican protein is shown in FIGS. 24I through 24K. In thisalignment (made using the ALIGN software {Myers and Miller (1989)CABIOS, ver. 2.0}; pam120.mat scoring matrix; gap opening penalty=12,gap extension penalty=4), the proteins are 75.5% identical, although itis seen that murine brevican protein includes a domain which does notoccur in TANGO 332 protein, this domain is present from about amino acidresidue 626 to the carboxyl terminus of murine brevican protein. Analignment of the nucleotide sequences of the ORFs encoding (human) TANGO332 and murine brevican protein is shown in FIGS. 24L through 24U. Thetwo ORFs are 62.6% identical, as assessed using the same software andparameters.

[0704] TANGO 332 exhibits many of the same properties as BEF. TANGO 332is also related to murine brevican protein, and thus is involved withcorresponding physiological processes (i.e., such as those describedabove) in humans. For example, TANGO 332 modulates intracellular bindingand migration of cells in a tissue or extracellular matrix. However, theabsence from BEF of one of the two extracellular link domains present inTANGO 332 indicates that one or more of the subunit structure, thetissue specificity, and the binding specificity of TANGO 332 and BEFproteins differ. Thus, TANGO 332 is involved in many of thephysiological processes and disorders in which BEF protein is involved.Like murine brevican and other proteoglycans, TANGO 332 acts in vivo asa tissue organizing protein, influences growth and maturation of tissuesin which it is expressed, modulates growth factor-mediated activities,modulates structural features of tissues (e.g., collagenfibrillogenesis), modulates tumor cell growth and invasivity, andinfluences neurite growth and branching.

[0705] The signal peptide prediction program SIGNALP (Nielsen et al.(1997) Protein Engineering 10:1-6) predicted that human TANGO 332protein includes an approximately 22 (i.e., 20, 21, 22, 23, or 24) aminoacid residue signal peptide (amino acid residues 1 to 22 of SEQ ID NO:331; SEQ ID NO: 332) preceding the mature TANGO 332 protein (i.e.,approximately amino acid residues 23 to 671 of SEQ ID NO: 331; SEQ IDNO: 333). Human TANGO 332 protein is a secreted protein, as assessedusing the secretion assay described herein. Secreted TANGO 332 proteinshaving approximate sizes of 148 kilodaltons and 100 kilodaltons could bedetected using this assay.

[0706]FIG. 24F depicts a hydrophobicity plot of human TANGO 332 protein.

[0707] Relatively hydrophobic regions are above the dashed horizontalline, and relatively hydrophilic regions are below the dashed horizontalline. The hydrophobic region which corresponds to amino acid residues 1to 22 of SEQ ID NO: 331 is the signal sequence of human TANGO 332 (SEQID NO: 332). As described elsewhere herein, relatively hydrophilicregions are generally located at or near the surface of a protein, andare more frequently effective immunogenic epitopes than are relativelyhydrophobic regions. For example, the region of human TANGO 332 proteinfrom about amino acid residue 445 to about amino acid residue 475appears to be located at or near the surface of the protein, while theregion from about amino acid residue 45 to about amino acid residue 62appears not to be located at or near the surface.

[0708] The predicted molecular weight of human TANGO 332 protein withoutmodification and prior to cleavage of the signal sequence is about 71.7kilodaltons. The predicted molecular weight of the mature human TANGO332 protein without modification and after cleavage of the signalsequence is about 69.5 kilodaltons.

[0709] Uses of TANGO 332 Nucleic Acids,

[0710] Polypeptides, and Modulators Thereof

[0711] TANGO 332 proteins are involved in disorders which affect bothtissues in which they are normally expressed and tissues in which theyare normally not expressed. Based on the observation that TANGO 332 isexpressed in human adult brain tissue, TANGO 332 protein is involved inone or more biological processes which occur in these tissues. Inparticular, TANGO 332 is involved in modulating growth, proliferation,survival, differentiation, and activity of cells including, but notlimited to, adult brain cells of the animal in which it is normallyexpressed. Thus, TANGO 332 has a role in disorders which affect thesecells and their growth, proliferation, survival, differentiation,interaction, and activity. Examples of such disorders include, by way ofexample and not limitation, disorders of neural connection establishmentor maintenance, impaired cognitive function, dementia, senility,Alzheimer's disease, mental retardation, brain tumors (e.g., gliomassuch as astrocytomas, endophytic and exophytic retinoblastomas,ependymomas, gangliogliomas, mixed gliomas, nasal gliomas, opticgliomas, and Schwannomas, and other brain cell tumors such asmedulloblastomas, pituitary adenomas, teratomas, etc.), and the like.TANGO 332 can also be involved in the other brain disorders describedelsewhere in this disclosure.

[0712] Homology of human TANGO 332 with murine brevican protein and withhuman brevican homolog BEF indicates that TANGO 332 has physiologicalfunctions in humans analogous to the functions of these proteins.Brevican is a member of the aggrecan/versican family of proteoglycans,and has a hyaluronic acid-binding domain in its amino terminal regionand a lectin-like domain in its carboxyl terminal region. Expression ofbrevican is highly specific to brain tissue, and increases as themammalian brain develops. Thus, brevican is involved in maintaining theextracellular environment of mature brain tissue and is a constituent ofadult brain extracellular matrix. TANGO 332 is involved in modulatingcell-to-cell adhesion, tissue and extracellular matrix invasivity ofcells, and the like. Thus, TANGO 332 is involved in disorders in whichthese physiological processes are relevant. Such disorders include, forexample, loss of control of cell growth, tumor metastasis, malformationof neurological connections, inflammation, immune and autoimmuneresponses, and the like.

[0713] In addition, presence in TANGO 332 of extracellular link domainsindicates that this protein is involved in physiological processesinvolving structure and function of extracellular matrices andinteraction of cells with such matrices and with each other. This isfurther evidence that TANGO 332 is involved in disorders such asinappropriate inflammation, tumor metastasis, inappropriate leukocyteextravasation, localization, and reactivity, and the like.

[0714] TANGO 332-related molecules can be used to modulate one or moreof the activities in which TANGO 332 is involved and can also be used toprevent, diagnose, or treat one or more of the disorders in which TANGO332 is involved.

[0715] TANGO 202

[0716] A cDNA clone (designated jthke096b05) encoding at least a portionof human TANGO 202 protein was isolated from a human fetal skin cDNAlibrary. The corresponding murine cDNA was isolated as a clone(designated jtmMa044f07) from a bone marrow stromal cell cDNA library.The human TANGO 202 protein is predicted by structural analysis to be atype I membrane protein, although it can exist in a secreted form aswell. The murine TANGO 202 protein is predicted by structural analysisto be a secreted protein.

[0717] The full length of the cDNA encoding human TANGO 202 protein(FIG. 25; SEQ ID NO: 371) is 1656 nucleotide residues. The open readingframe (ORF) of this cDNA, nucleotide residues 34 to 1458 of SEQ ID NO:371 (i.e., SEQ ID NO: 372), encodes a 475-amino acid transmembraneprotein (FIG. 25; SEQ ID NO: 373).

[0718] The invention thus includes purified human TANGO 202 protein,both in the form of the immature 475 amino acid residue protein (SEQ IDNO: 373) and in the form of the mature 456 amino acid residue protein(SEQ ID NO: 375). The invention also includes purified murine TANGO 202protein, both in the form of the immature 470 amino acid residue protein(SEQ ID NO: 439) and in the form of the mature 451 amino acid residueprotein (SEQ ID NO: 413). Mature human or murine TANGO 202 proteins canbe synthesized without the signal sequence polypeptide at the aminoterminus thereof, or they can be synthesized by generating immatureTANGO 202 protein and cleaving the signal sequence therefrom.

[0719] The invention includes nucleic acid molecules which encode apolypeptide of the invention. Such nucleic acids include, for example, aDNA molecule having the nucleotide sequence listed in SEQ ID NO: 371 orsome portion thereof or SEQ ID NO: 439 or some portion thereof, such asthe portion which encodes mature human or murine TANGO 202 protein,immature human or murine TANGO 202 protein, or a domain of human ormurine TANGO 202 protein. These nucleic acids are collectively referredto as nucleic acids of the invention.

[0720] TANGO 202 proteins and nucleic acid molecules encoding themcomprise a family of molecules having certain conserved structural andfunctional features.

[0721] A common domain present in TANGO 202 proteins is a signalsequence. In one embodiment, a TANGO 202 protein contains a signalsequence corresponding to amino acid residues 1 to 19 of SEQ ID NO: 373(SEQ ID NO: 374) or to amino acid residues 1 to 19 of SEQ ID NO: 439(SEQ ID NO: 412). The signal sequence is cleaved during processing ofthe mature protein.

[0722] TANGO 202 proteins can also include an extracellular domain. Thehuman TANGO 202 protein extracellular domain is located from about aminoacid residue 20 to about amino acid residue 392 of SEQ ID NO: 373 in thenon-secreted form, and from about amino acid residue 20 to amino acidresidue 475 of SEQ ID NO: 373 (i.e., the entire mature human protein).The murine TANGO 202 protein extracellular domain is located from aboutamino acid residue 20 to amino acid residue 470 of SEQ ID NO: 439 (i.e.,the entire mature murine protein).

[0723] TANGO 202 proteins of the invention can also include atransmembrane domain. As used herein, a “transmembrane domain” refers toan amino acid sequence having at least about 20 to 25 amino acidresidues in length and which contains at least about 65-70% hydrophobicamino acid residues such as alanine, leucine, phenylalanine, protein,tyrosine, tryptophan, or valine. In a preferred embodiment, atransmembrane domain contains at least about 15 to 30 amino acidresidues, preferably about 20-25 amino acid residues, and has at leastabout 60-80%, more preferably 65-75%, and more preferably at least about70% hydrophobic residues. Thus, in one embodiment, a TANGO 202 proteinof the invention contains a transmembrane domain corresponding to aboutamino acid residues 393 to 415 of SEQ ID NO: 373 (SEQ ID NO: 377).

[0724] In addition, TANGO 202 proteins of the invention can include acytoplasmic domain, particularly including a carboxyl-terminalcytoplasmic domain. The cytoplasmic domain is located from about aminoacid residue 416 to amino acid residue 475 of SEQ ID NO: 373 (SEQ ID NO:378) in the non-secreted form of human TANGO 202 protein.

[0725] TANGO 202 proteins typically comprise a variety of potentialpost-translational modification sites (often within an extracellulardomain), such as those described herein in Tables XXIV (for human TANGO202) and XXV (for murine TANGO 202), as predicted by computerizedsequence analysis of TANGO 202 proteins using amino acid sequencecomparison software (comparing the amino acid sequence of TANGO 202 withthe information in the PROSITE database {rel. 12.2; February 1995} andthe Hidden Markov Models database {Rel. PFAM 3.3}). TABLE XXIV AminoAcid Type of Potential Modification Site Residues Amino Acid or Domainof SEQ ID NO: 373 Sequence N-glycosylation site 47 to 50 NWTA 61 to 64NETF 219 to 222 NYSA 295 to 298 NVSL 335 to 338 NQTV 347 to 350 NLSVProtein kinase C phosphorylation site 70 to 72 TLK 137 to 139 TSK 141 to143 SNK 155 to 157 SQR 238 to 240 TGR 245 to 247 TIR 277 to 279 THR 307to 309 SDR 355 to 357 SSK 387 to 389 SHR 418 to 420 TFK 421 to 423 SHRCasein kinase II phosphorylation site 337 to 340 TVAE 438 to 441 TSGE464 to 467 SQQD N-myristoylation site 53 to 58 GGKPCL 120 to 125 GNLGCY136 to 141 GTSKTS 162 to 167 GMESGY 214 to 219 GACGGN Kringle domainsignature 85 to 90 YCRNPD Kringle Domain  34 to 116 See FIG. 25 CUBdomain 216 to 320 See FIG. 25

[0726] TABLE XXV Amino Acid Type of Potential Modification Site Residuesof Amino Acid or Domain SEQ ID NO: 439 Sequence N-glycosylation site 59to 62 NETF 217 to 220 NYSA 255 to 258 NFTL 293 to 296 NVSL 333 to 336NQTL 345 to 348 NLSV cAMP- or cGMP-dependent protein 455 to 458 RRSSkinase phosphorylation site Protein kinase C phosphorylation site 68 to70 TLK 135 to 137 TSK 139 to 141 SNK 153 to 155 SQR 236 to 238 TGR 243to 245 TIR 275 to 277 THR 283 to 285 SGR 305 to 307 SDR 353 to 355 SSK408 to 410 SQR 453 to 455 SLR 457 to 459 SSR Casein kinase IIphosphorylation site 28 to 31 SGPE 257 to 260 TLFD 321 to 324 TKEE 335to 338 TLAE 384 to 387 TATE N-myristoylation site 51 TO 56 GGKPCL 118 TO123 GNLGCY 134 TO 139 GTSKTS 160 TO 165 GMESGY 212 TO 217 GACGGN 391 TO396 GLCTAW 429 TO 434 GTVVSL Kringle domain signature 83 to 88 YCRNPDKringle Domain  32 to 114 See FIG. 25 CUB domain 214 to 318 See FIG. 25

[0727] In various embodiments, the protein of the invention has at least1, 2, 4, 6, 10, 15, or 20 or more of the post-translational modificationsites described herein in Tables XXIV and XXV.

[0728] Examples of additional domains present in human and murine TANGO202 protein include Kringle domains and CUB domains. In one embodiment,the protein of the invention has at least one domain that is at least55%, preferably at least about 65%, more preferably at least about 75%,yet more preferably at least about 85%, and most preferably at leastabout 95% identical to one of the domains described herein in TablesXXIV and XXV. Preferably, the protein of the invention has at least oneKringle domain and one CUB domain.

[0729] A Kringle domain has a characteristic profile that has beendescribed in the art (Castellino and Beals (1987) J. Mol. Evol.26:358-369; Patthy (1985) Cell 41:657-663; Ikeo et al. (1991) FEBS Lett.287:146-148). Many, but not all, Kringle domains comprise a conservedhexapeptide signature sequence, namely

[0730] (F or Y)—C—R—N—P—(D or N or R) (SEQ ID NO: 455).

[0731] The cysteine residue is involved in a disulfide bond.

[0732] Kringle domains are triple-looped, disulfide cross-linked domainsfound in a varying number of copies in, for example, some serineproteases and plasma proteins. Kringle domains have a role in bindingmediators (e.g., membranes, other proteins, or phospholipids) and inregulation of proteolytic activity. Kringle domains have been identifiedin the following proteins, for example: apolipoprotein A, bloodcoagulation factor XII (Hageman factor), hepatocyte growth factor (HGF),HGF-like protein (Friezner Degen et al., (1991) Biochemistry30:9781-9791), HGF activator (Miyazawa et al., (1993) J. Biol. Chem.268:10024-10028), plasminogen, thrombin, tissue plasminogen activator,urokinase-type plasminogen activator, and four influenza neuramimidases.The presence of a Kringle domain in each of human and murine TANGO 202protein indicates that TANGO 202 is involved in one or morephysiological processes in which these other Kringle domain-containingproteins are involved, has biological activity in common with one ormore of these other Kringle domain-containing proteins, or both.

[0733] CUB domains are extracellular domains of about 110 amino acidresidues which occur in functionally diverse, mostly developmentallyregulated proteins (Bork and Beckmann (1993) J. Mol. Biol. 231:539-545;Bork (1991) FEBS Lett. 282:9-12). Many CUB domains contain fourconserved cysteine residues, although some, like that of TANGO 202,contain only two of the conserved cysteine residues. The structure ofthe CUB domain has been predicted to assume a beta-barrel configuration,similar to that of immunoglobulins. Other proteins which have been foundto comprise one or more CUB domains include, for example, mammaliancomplement sub-components Cls and Clr, hamster serine protease Casp,mammalian complement activating component of Ra-reactive factor,vertebrate enteropeptidase, vertebrate bone morphogenic protein 1, seaurchin blastula proteins BP10 and SpAN, Caenorhabditis eleganshypothetical proteins F42A10.8 and R151.5, neuropilin (A5 antigen), seaurchin fibropellins I and III, mammalian hyaluronate-binding proteinTSG-6 (PS4), mammalian spermadhesins, and Xenopus embryonic proteinUVS.2. The presence of a CUB domain in each of human and murine TANGO202 protein indicates that TANGO 202 is involved in one or morephysiological processes in which these other CUB domain-containingproteins are involved, has biological activity in common with one ormore of these other CUB domain-containing proteins, or both.

[0734] The signal peptide prediction program SIGNALP (Nielsen et al.(1997) Protein Engineering 10: 1-6) predicted that human TANGO 202protein includes a 19 amino acid signal peptide (amino acid residues 1to 19 of SEQ ID NO: 373; SEQ ID NO: 374) preceding the mature TANGO 202protein (amino acid residues 20 to 475 of SEQ ID NO: 373; SEQ ID NO:375). Human TANGO 202 protein includes an extracellular domain (aminoacid residues 20 to 392 of SEQ ID NO: 373; SEQ ID NO: 376); atransmembrane domain (amino acid residues 393 to 415 of SEQ ID NO: 373;SEQ ID NO: 377); and a cytoplasmic domain (amino acid residues 416 to475 of SEQ ID NO: 373; SEQ ID NO: 378). The murine homolog of TANGO 202protein is predicted to be a secreted protein. Thus, it is recognizedthat human TANGO 202 can also exist in the form of a secreted protein,likely being translated from an alternatively spliced TANGO 202 mRNA. Ina variant form of the protein, an extracellular portion of TANGO 202protein (e.g., amino acid residues 20 to 392 of SEQ ID NO: 373) can becleaved from the mature protein to generate a soluble fragment of TANGO202.

[0735]FIG. 25L depicts a hydrophobicity plot of human TANGO 202 protein.Relatively hydrophobic regions are above the dashed horizontal line, andrelatively hydrophilic regions are below the dashed horizontal line. Thehydrophobic region which corresponds to amino acid residues 1 to 19 ofSEQ ID NO: 373 is the signal sequence of human TANGO 202 (SEQ ID NO:374). The hydrophobic region which corresponds to amino acid residues393 to 415 of SEQ ID NO: 373 is the transmembrane domain of human TANGO202 (SEQ ID NO: 377). As described elsewhere herein, relativelyhydrophilic regions are generally located at or near the surface of aprotein, and are more frequently effective immunogenic epitopes than arerelatively hydrophobic regions. For example, the region of human TANGO202 protein from about amino acid residue 61 to about amino acid residue95 appears to be located at or near the surface of the protein, whilethe region from about amino acid residue 395 to about amino acid residue420 appears not to be located at or near the surface.

[0736] The predicted molecular weight of human TANGO 202 protein withoutmodification and prior to cleavage of the signal sequence is about 51.9kilodaltons. The predicted molecular weight of the mature human TANGO202 protein without modification and after cleavage of the signalsequence is about 50.1 kilodaltons.

[0737] The full length of the cDNA encoding murine TANGO 202 protein(FIG. 25; SEQ ID NO: 437) is 4928 nucleotide residues. The ORF of thiscDNA, nucleotide residues 81 to 1490 of SEQ ID NO: 437 (i.e., SEQ ID NO:438), encodes a 470-amino acid secreted protein (FIG. 25; SEQ ID NO:439).

[0738] The signal peptide prediction program SIGNALP (Nielsen et al.(1997) Protein Engineering 10:1-6) predicted that murine TANGO 202protein includes a 19 amino acid signal peptide (amino acid residues 1to 19 of SEQ ID NO: 439; SEQ ID NO: 412) preceding the mature TANGO 202protein (amino acid residues 20 to 470 of SEQ ID NO: 439; SEQ ID NO:413). Murine TANGO 202 protein is a secreted protein.

[0739]FIG. 25M depicts a hydrophobicity plot of murine TANGO 202protein. Relatively hydrophobic regions are above the dashed horizontalline, and relatively hydrophilic regions are below the dashed horizontalline. The hydrophobic region which corresponds to amino acid residues 1to 19 of SEQ ID NO: 439 is the signal sequence of murine TANGO 202 (SEQID NO: 412). As described elsewhere herein, relatively hydrophilicregions are generally located at or near the surface of a protein, andare more frequently effective immunogenic epitopes than are relativelyhydrophobic regions. For example, the region of murine TANGO 202 proteinfrom about amino acid residue 61 to about amino acid residue 95 appearsto be located at or near the surface of the protein, while the regionfrom about amino acid residue 295 to about amino acid residue 305appears not to be located at or near the surface

[0740] The predicted molecular weight of murine TANGO 202 proteinwithout modification and prior to cleavage of the signal sequence isabout 51.5 kilodaltons. The predicted molecular weight of the maturemurine TANGO 202 protein without modification and after cleavage of thesignal sequence is about 49.7 kilodaltons.

[0741] Human and murine TANGO 202 proteins exhibit considerable sequencesimilarity, as indicated herein in FIGS. 25J and 25K. FIGS. 25J and 25Kdepict an alignment of human and murine TANGO 202 amino acid sequences(SEQ ID NOs: 373 and 439, respectively). In this alignment (made usingthe ALIGN software {Myers and Miller (1989) CABIOS, ver. 2.0};pam120.mat scoring matrix; gap penalties −12/−4), the proteins are 76.5%identical. The human and murine ORFs encoding TANGO 202 are 87.4%identical, as assessed using the same software and parameters.

[0742] In situ hybridization experiments in mouse tissues indicated thatmRNA corresponding to the cDNA encoding TANGO 202 is expressed in thetissues listed in Table XXVI, wherein “+” indicates detectableexpression and “++” indicates a greater level of expression than “+”.TABLE XXVI Relative Level of Animal Tissue Expression Mouse bladder,especially in ++ (Adult) transitional epithelium renal glomeruli +brain + heart + liver + spleen + placenta + Mouse ubiquitous + (Embryo)

[0743] Uses of TANGO 202 Nucleic Acids,

[0744] Polypeptides, and Modulators Thereof

[0745] TANGO 202 proteins are involved in disorders which affect bothtissues in which they are normally expressed and tissues in which theyare normally not expressed. Based on the observation that TANGO 202 isexpressed in human fetal skin, ubiquitously in fetal mouse tissues, inadult murine bone marrow stromal cells, and in cells of adult murinebladder, renal glomeruli, brain, heart, liver, spleen and placenta,TANGO 202 protein is involved in one or more biological processes whichoccur in these tissues. In particular, TANGO 202 is involved inmodulating growth, proliferation, survival, differentiation, andactivity of cells of these tissues including, but not limited to,hematopoietic and fetal cells. Thus, TANGO 202 has a role in disorderswhich affect these cells and their growth, proliferation, survival,differentiation, and activity. Ubiquitous expression of TANGO 202 infetal murine tissues, contrasted with limited expression in adult murinetissues further indicates that TANGO 202 is involved in disorders inwhich it is inappropriately expressed (e.g., disorders in which TANGO202 is expressed in adult murine tissues other than bone marrow stromalcells and disorders in which TANGO 202 is not expressed in one or moredeveloping fetal tissues).

[0746] The presence of a Kringle domain in both the murine and humanTANGO 202 proteins indicates that this protein is involved in modulatingcellular binding to one or more mediators (e.g., proteins,phospholipids, intracellular organelles, or other cells), in modulatingproteolytic activity, or both. The presence of a Kringle domain in otherproteins (e.g., growth factors) indicates activities that these proteinsshare with TANGO 202 protein (e.g., modulating cell dissociation andmigration into and through extracellular matrices). The presence ofKringle domains in numerous plasma proteins, particularly coupled withthe observation that TANGO 202 is expressed in adult murine bone marrowstromal cells, indicates a role for TANGO 202 protein in modulatingbinding of blood or hematopoietic cells (or both) to one or moremediators. Thus, TANGO 202 is involved in disorders relating to aberrantcellular protease activity, inappropriate interaction or non-interactionof cells with mediators, and in blood and hematopoietic cell-relateddisorders. Such disorders include, by way of example and not limitation,immune disorders, infectious diseases, auto-immune disorders, vascularand cardiovascular disorders, disorders related to mal-expression ofgrowth factors, cancers, hematological disorders, and the like.

[0747] The cDNA encoding TANGO 202 exhibits significant nucleotidesequence similarity with a polynucleotide encoding akringle-domain-containing protein (designated HTHBZ47) described in theEuropean Patent Application No. EP 0 911 399 A2 (published Apr. 28,1999). Thus, the TANGO 202 protein can exhibit one or more of theactivities exhibited by HTHBZ47, and can be used to prevent, inhibit,diagnose, and treat one or more disorders for which HTHBZ47 is useful.These disorders include cancer, inflammation, autoimmune disorders,allergic disorders, asthma, rheumatoid arthritis, inflammation ofcentral nervous system tissues, cerebellar degeneration, Alzheimer'sdisease, Parkinson's disease, multiple sclerosis, amylotrophic lateralsclerosis, head injury damage and other neurological abnormalities,septic shock, sepsis, stroke, osteoporosis, osteoarthritis, ischemicreperfusion injury, cardiovascular disease, kidney disease, liverdisease, ischemic injury, myocardial infarction, hypotension,hypertension, AIDS, myelodysplastic syndromes and other hematologicabnormalities, aplastic anemia, male pattern baldness, and bacterial,fungal, protozoan, and viral infections.

[0748] The presence of a CUB domain in both the murine and human TANGO202 proteins indicates that this protein is involved in biologicalprocesses common to other CUB domain-containing proteins, such asdevelopmental processes and binding to mediators. Therefore, TANGO 202protein has a role in disorders which involve inappropriatedevelopmental processes (e.g., abnormally high proliferation orun-differentiation of a differentiated tissue or abnormally lowdifferentiation or proliferation of a non-developed ornon-differentiated tissue) and modulation of cell growth, proliferation,survival, differentiation, and activity. Such disorders include, by wayof example and not limitation, various cancers and birth anddevelopmental defects.

[0749] Thus, proteins and nucleic acids of the invention which areidentical to, similar to, or derived from human and murine TANGO 202proteins and nucleic acids encoding them are useful for preventing,diagnosing, and treating, among others, vascular and cardiovasculardisorders, hematological disorders, disorders related to mal-expressionof growth factors, and cancer. Other uses for these proteins and nucleicacids of the invention relate to modulating cell growth (e.g.,angiogenesis), proliferation (e.g., cancers), survival (e.g.,apoptosis), differentiation (e.g., hematopoiesis), and activity (e.g.,ligand-binding capacity). TANGO 202 proteins and nucleic acids encodingthem are also useful for modulating cell dissociation and modulatingmigration of cells in extracellular matrices.

[0750] TANGO 234

[0751] A cDNA clone (designated jthsa104d11) encoding at least a portionof human TANGO 234 protein was isolated from a human fetal spleen cDNAlibrary. The human TANGO 234 protein is predicted by structural analysisto be a transmembrane protein, although it can exist in a secreted formas well.

[0752] The full length of the cDNA encoding human TANGO 234 protein(FIG. 26; SEQ ID NO: 379) is 4628 nucleotide residues. The ORF of thiscDNA, nucleotide residues 28 to 4386 of SEQ ID NO: 379 (i.e., SEQ ID NO:380), encodes a 1453-amino acid transmembrane protein (FIG. 26; SEQ IDNO: 381).

[0753] The invention thus includes purified human TANGO 234 protein,both in the form of the immature 1453 amino acid residue protein (SEQ IDNO: 381) and in the form of the mature 1413 amino acid residue protein(SEQ ID NO: 383). Mature human TANGO 234 protein can be synthesizedwithout the signal sequence polypeptide at the amino terminus thereof,or it can be synthesized by generating immature TANGO 234 protein andcleaving the signal sequence therefrom.

[0754] The invention includes nucleic acid molecules which encode apolypeptide of the invention. Such nucleic acids include, for example, aDNA molecule having the nucleotide sequence listed in SEQ ID NO: 379 orsome portion thereof, such as the portion which encodes mature TANGO 234protein, immature TANGO 234 protein, or a domain of TANGO 234 protein.These nucleic acids are collectively referred to as nucleic acids of theinvention.

[0755] TANGO 234 proteins and nucleic acid molecules encoding themcomprise a family of molecules having certain conserved structural andfunctional features, as indicated by the conservation of amino acidsequence between human TANGO 234 protein and bovine WC1 protein, asshown in FIGS. 26K through 26P, and the conservation of nucleotidesequence between the ORFs encoding human TANGO 234 protein and bovineWC1 protein, as shown in FIGS. 26Q-1 through 26Q-19.

[0756] A common domain present in TANGO 234 proteins is a signalsequence. In one embodiment, a TANGO 234 protein contains a signalsequence corresponding to amino acid residues 1 to 40 of SEQ ID NO: 381(SEQ ID NO: 382). The signal sequence is cleaved during processing ofthe mature protein.

[0757] TANGO 234 proteins can include an extracellular domain. The humanTANGO 234 protein extracellular domain is located from about amino acidresidue 41 to about amino acid residue 1359 of SEQ ID NO: 381. TANGO 234can alternately exist in a secreted form, such as a mature proteinhaving the amino acid sequence of amino acid residues 41 to 1453 orresidues 41 to about 1359 of SEQ ID NO: 381.

[0758] In addition, TANGO 234 include a transmembrane domain. In oneembodiment, a TANGO 234 protein of the invention contains atransmembrane domain corresponding to about amino acid residues 1360 to1383 of SEQ ID NO: 381 (SEQ ID NO: 385).

[0759] The present invention includes TANGO 234 proteins having acytoplasmic domain, particularly including proteins having acarboxyl-terminal cytoplasmic domain. The human TANGO 234 cytoplasmicdomain is located from about amino acid residue 1384 to amino acidresidue 1453 of SEQ ID NO: 381 (SEQ ID NO: 386).

[0760] TANGO 234 proteins typically comprise a variety of potentialpost-translational modification sites (often within an extracellulardomain), such as those described herein in Table XXVII, as predicted bycomputerized sequence analysis of TANGO 234 proteins using amino acidsequence comparison software (comparing the amino acid sequence of TANGO234 with the information in the PROSITE database {rel. 12.2; February1995} and the Hidden Markov Models database {Rel. PFAM 3.3}). In certainembodiments, a protein of the invention has at least 1, 2, 4, 6, 10, 15,or 20 or more of the post-translational modification sites listed inTable XXVII. TABLE XXVII Amino Acid Type of Potential Modification SiteResidues of Amino Acid or Domain SEQ ID NO: 381 Sequence N-glycosylationsite 42 to 45 NGTD 78 to 81 NTTA 120 to 123 NESA 161 to 164 NNSC 334 to337 NESF 377 to 380 NCSG 441 to 444 NESA 548 to 551 NESN 637 to 640 NAST972 to 975 NESL 1013 to 1016 NVSD 1084 to 1087 NATV 1104 to 1107 NCTG1161 to 1164 NGTW 1171 to 1174 NITT 1318 to 1321 NESF 1354 to 1357 NASSGlycosaminoglycan attachment site 558 to 561 SGWG 665 to 668 SGWG cAMP-or cGMP-dependent protein 1229 to 1232 RRIS kinase phosphorylation site1399 to 1402 RRGS Protein kinase C phosphorylation site 165 to 167 SGR268 to 270 TNR 379 to 381 SGR 419 to 421 SRR 469 to 471 SDK 506 to 508STR 589 to 591 SNR 593 to 595 SGR 661 to 663 SCR 696 to 698 SSR 746 to748 TER 805 to 807 SGR 815 to 817 TWR 959 to 961 SVR 1256 to 1258 SGR1349 to 1351 SLK 1396 to 1398 STR Casein kinase II phosphorylation site44 to 47 TDLE 71 to 74 TVCD 178 to 181 TICD 245 to 248 SHNE 253 to 256TCYD 258 to 261 SDLE 319 to 322 SGSD 332 to 335 SGNE 392 to 395 TICD 439to 442 TGNE 606 to 609 TVCD 622 to 625 SQLD 673 to 676 SHSE 686 to 689SDME 760 to 763 TGGE 765 to 768 SLWD 818 to 821 SVCD 845 to 848 SVGD 857to 860 TWAE 907 to 910 SQCD 923 to 926 SLCD 927 to 930 THWD 974 to 977SLLD 1059 to 1062 TICD 1106 to 1109 TGTE 1145 to 1148 SETE 1233 to 1236SPAE 1241 to 1244 TCED 1269 to 1272 TVCD 1402 to 1405 SLEE 1425 to 1428TSDD N-myristoylation site 67 to 72 GQWGTV 90 to 95 GCPFSF 101 to 106GQAVTR 119 to 124 GNESAL 133 to 138 GSHNCY 160 to 165 GNNSCS 197 to 202GCPSSF 226 to 231 GNELAL 240 to 245 GNHDCS 267 to 272 GTNRCM 304 to 309GCGTAL 328 to 333 GVSCSG 374 to 379 GSNNCS 411 to 416 GCPFSV 418 to 423GSRRAK 440 to 445 GNESAL 465 to 470 GVICSD 547 to 552 GNESNI 588 to 593GSNRCS 632 to 637 GMGLGN 668 to 673 GNNDCS 679 to 684 GVICSD 695 to 700GTWGSV 712 to 717 GCGENG 720 to 725 GSWGTV 758 to 763 GCGSAL 853 to 858GQGTGT 891 to 896 GQSDCG 944 to 949 GVRCSG 985 to 990 GTRTSD 992 to 997GCEDAS 1078 to 1083 GVLPAS 1121 to 1126 GSSRCA 1132 to 1137 GILCAN 1162to 1167 GMNIAE 1185 to 1190 GCTGGE 1265 to 1270 GNGLTW 1288 to 1293GVVCSR 1302 to 1307 GTALST 1331 to 1336 GAPPCI 1342 to 1347 GNTVSV 1422to 1427 GCGVAF 1443 to 1438 GQHDCR 1444 to 1449 GVICSE Amidation site1167 to 1170 VGRR Speract receptor repeated (SRR) 53 to 90 See FIG. 26domain signature 160 to 197 See FIG. 26 267 to 304 See FIG. 26 1041 to1078 See FIG. 26 1251 to 1288 See FIG. 26 Scavenger receptorcysteine-rich  51 to 148 See FIG. 26 (SRCR) domain 158 to 255 See FIG.26 265 to 362 See FIG. 26 372 to 469 See FIG. 26 479 to 576 See FIG. 26586 to 683 See FIG. 26 693 to 790 See FIG. 26 798 to 895 See FIG. 26 903 to 1000 See FIG. 26 1039 to 1136 See FIG. 26 1146 to 1243 See FIG.26 1249 to 1346 See FIG. 26

[0761] Among the domains that occur in TANGO 234 protein are SRR domainsand SRCR domains. In one embodiment, the protein of the invention has atleast one domain that is at least 55%, preferably at least about 65%,more preferably at least about 75%, yet more preferably at least about85%, and most preferably at least about 95% identical to one of thesedomains. In other embodiments, the protein has at least two of the SRRand SRCR domains described herein in Table XXVII. In other embodiments,the protein has at least one SRR domain and at least one SRCR domain.

[0762] The SRR domain is named after a receptor domain identified in asea urchin egg protein designated speract. The consensus sequence ofthis domain (using standard one-letter amino acid codes, wherein X isany amino acid residue) is as follows. -G-X₅-G-X₂-E-X₆—W-G-X₂—C—X₃—(F orY or W)-X₈—C—X₃-G-(SEQ ID NO: 456).

[0763] Speract is a transmembrane glycoprotein of 500 amino acidresidues (Dangott et al. (1989) Proc. Natl. Acad. Sci. USA86:2128-2132). Structurally, this receptor consists of a largeextracellular domain of 450 residues, followed by a transmembrane regionand a small cytoplasmic domain of 12 amino acid residues. Theextracellular domain contains four repeats of an approximately 115 aminoacid domain. There are 17 amino acid residues that are perfectlyconserved in the four repeats in speract, including six cysteineresidues, six glycine residues, and two glutamate residues. TANGO 234has five SRR domains, in which 16 of the 17 conserved speract residuesare present of four of the SRR domains and 15 are present in theremaining SRR domain. This domain is designated the speract receptorrepeated domain. The amino acid sequence of mammalian macrophagescavenger receptor type I (MSR1) exhibits such a domain (Freeman et al.(1990) Proc. Natl. Acad. Sci. USA 87:8810-8814). MSRI proteins aremembrane glycoproteins implicated in the pathologic deposition ofcholesterol in arterial walls during atherogenesis. TANGO 234 isinvolved in one or more physiological processes related to cholesteroldeposition and atherogenesis, as well as other vascular andcardiovascular disorders.

[0764] Scavenger receptor cysteine-rich (SRCR) domains are disulfiderich extracellular domains which are present in certain cell surface andsecreted proteins. Proteins having SRCR domains exhibit diverse ligandbinding specificity. For example, in addition to modified lipoproteins,some of these proteins bind a variety of surface components ofpathogenic microorganisms, and some of the proteins bind apoptoticcells. SRCR domains are also involved in mediating immune developmentand response. Other SRCR-containing proteins are involved in binding ofmodified lipoproteins (e.g., oxidized low density lipoprotein {LDL}) byspecialized macrophages, leading to the formation of macrophages filledwith cholesteryl ester droplets (i.e., foam cells). TANGO 234 isinvolved in one or more physiological processes in which these otherSRCR domain-containing proteins are involved, such as LDL uptake andmetabolism, regulation of serum cholesterol level, atherogenesis,atherosclerosis, bacterial or viral infections, immune development, andgeneration and perseverance of immune responses.

[0765] WC1 is a ruminant protein having an SRCR domain. WC1 and gammadelta T-cell receptor are the only known gamma delta T-cell specificantigens. Antibodies which bind specifically with WC1 induce growtharrest in IL-2-dependent gamma delta T-cell and augment proliferation ofgamma delta T-cells in an autologous mixed lymphocyte reaction or in thepresence of anti-CD2 or anti-CD5 antibodies. Injection of antibodieswhich bind specifically with WC1 into calves results in long-lastingdepletion of gamma delta T-cells. Furthermore, antibodies which bindspecifically with WC1 can be used to purify gamma delta T-cells.

[0766] Gamma delta T-cells are involved in a variety of physiologicalprocesses. For example, these cells are potential mediators of allergicairway inflammation and lyme disease. Furthermore, these cells areinvolved in natural resistance to viral infections and can mediateautoimmune diseases. Elimination of gamma delta T-cells by injection ofantibodies which bind specifically therewith can affect the outcomes ofthese disorders.

[0767] TANGO 234 is likely the human orthologue of ruminant protein WC1,and thus is involved with the physiological processes described above inhumans. An alignment of the amino acid sequences of (human) TANGO 234and bovine WC1 protein is shown in FIGS. 26K-26P. In this alignment(made using the ALIGN software {Myers and Miller (1989) CABIOS, ver.2.0}; pam120.mat scoring matrix; gap penalties −12/−4), the proteins are40.4% identical. An alignment of the nucleotide sequences of the ORFsencoding (human) TANGO 234 and bovine WC1 protein is shown in FIGS.26Q-1 to 26Q-19. The two ORFs are 54.3% identical, as assessed using thesame software and parameters.

[0768] The signal peptide prediction program SIGNALP (Nielsen et al.(1997) Protein Engineering 10:1-6) predicted that human TANGO 234protein includes a 40 amino acid signal peptide (amino acid residues 1to 40 of SEQ ID NO: 381; SEQ ID NO: 382) preceding the mature TANGO 234protein (amino acid residues 41 to 4386 of SEQ ID NO: 381; SEQ ID NO:383). Human TANGO 234 protein includes an extracellular domain (aminoacid residues 41 to 1359 of SEQ ID NO: 381; SEQ ID NO: 384); atransmembrane domain (amino acid residues 1360 to 1383 of SEQ ID NO:381; SEQ ID NO: 385); and a cytoplasmic domain (amino acid residues 1384to 1453 of SEQ ID NO: 381; SEQ ID NO: 386).

[0769]FIG. 26J depicts a hydrophobicity plot of human TANGO 234 protein.Relatively hydrophobic regions are above the dashed horizontal line, andrelatively hydrophilic regions are below the dashed horizontal line. Thehydrophobic region which corresponds to amino acid residues 1 to 40 ofSEQ ID NO: 381 is the signal sequence of human TANGO 234 (SEQ ID NO:382). The hydrophobic region which corresponds to amino acid residues1360 to 1383 of SEQ ID NO: 381 is the transmembrane domain of humanTANGO 234 (SEQ ID NO: 385). As described elsewhere herein, relativelyhydrophilic regions are generally located at or near the surface of aprotein, and are more frequently effective immunogenic epitopes than arerelatively hydrophobic regions. For example, the region of human TANGO234 protein from about amino acid residue 225 to about amino acidresidue 250 appears to be located at or near the surface of the protein,while the region from about amino acid residue 990 to about amino acidresidue 1000 appears not to be located at or near the surface.

[0770] The predicted molecular weight of human TANGO 234 protein withoutmodification and prior to cleavage of the signal sequence is about 159.3kilodaltons. The predicted molecular weight of the mature human TANGO234 protein without modification and after cleavage of the signalsequence is about 154.7 kilodaltons.

[0771] Chromosomal mapping to identify the location of the gene encodinghuman TANGO 234 protein indicated that the gene was located atchromosomal location h12 p13 (with synteny to mo6). Flanking chromosomalmarkers include WI-6980 and GATA8A09.43. Nearby human loci include IBD2(inflammatory bowel disease 2), FPF (familial periodic fever), and HPDR2(hypophosphatemia vitamin D resistant rickets 2). Nearby genes are KLRC(killer cell receptor cluster), DRPLA (dentatorubro-pallidoluysianatrophy), GAPD (glyceraldehyde-3-phosphate) dehydrogenase, and PXR1(peroxisome receptor 1). Murine chromosomal mapping indicated that themurine orthologue is located near the scr (scruffy) locus. Nearby mousegenes include drpla (dentatorubral phillidoluysian atrophy), prp(proline rich protein), and kap (kidney androgen regulated protein).

[0772] Northern analysis experiments indicated that mRNA correspondingto the cDNA encoding TANGO 234 is expressed in the tissues listed inTable XXVIII, wherein “++” indicates moderate expression, “+” indicateslower expression, and “−” indicates no detectable expression. TABLEXXVIII Animal Tissue Relative Level of Expression Human spleen ++ fetallung ++ lung + thymus + bone marrow − peripheral blood leukocytes −

[0773] Uses of TANGO 234 Nucleic Acids,

[0774] Polypeptides, and Modulators Thereof

[0775] TANGO 234 proteins are involved in disorders which affect bothtissues in which they are normally expressed and tissues in which theyare normally not expressed. Based on the observation that TANGO 234 isexpressed in human fetal lung, spleen, and, to a lesser extent in adultlung and thymus tissue, TANGO 234 protein is involved in one or morebiological processes which occur in these tissues. In particular, TANGO234 is involved in modulating growth, proliferation, survival,differentiation, and activity of cells including, lung, spleen, thymus,bone marrow, hematopoietic, peripheral blood leukocytes, and fetal cellsof the animal in which it is normally expressed. Thus, TANGO 234 has arole in disorders which affect these cells and their growth,proliferation, survival, differentiation, and activity. TANGO 234 canhave a role in the lung, spleen, and hematological described elsewherein this disclosure. Expression of TANGO 234 in an animal is alsoinvolved in modulating growth, proliferation, survival, differentiation,and activity of cells and viruses which are foreign to the host (i.e.,bacterial, fungal, and viral infections).

[0776] Homology of human TANGO 234 with bovine WC1 protein indicatesthat TANGO 234 has physiological functions in humans analogous to thefunctions of WC1 in ruminants. Thus, TANGO 234 is involved in modulatinggrowth, proliferation, survival, differentiation, and activity of gammadelta T cells. For example, TANGO 234 affects the ability of gamma deltaT cells to interact with chemokines such as interleukin-2. TANGO 234therefore is involved in the physiological processes associated withallergic airway inflammation, lyme arthritis, resistance to viralinfection, auto-immune diseases, and the like.

[0777] In addition, presence in TANGO 234 of SRR and SRCR domainsindicates that TANGO 234 is involved in physiological functionsidentical or analogous to the functions performed by other proteinshaving such domains. For example, like other SRR domain-containingproteins, TANGO 234 modulates cholesterol deposition in arterial walls,and is thus involved in development and persistence of atherogenesis andarteriosclerosis, as well as other vascular and cardiovasculardisorders. Like other SRCR domain-containing proteins, TANGO 234 isinvolved in uptake and metabolism of LDL, regulation of serumcholesterol level, and can modulate these processes as well as theprocesses of atherogenesis, arteriosclerosis, immune development, andgeneration and perseverance of immune responses to bacterial, fungal,and viral infections.

[0778] TANGO 265

[0779] A cDNA clone (designated jthsa079g01) encoding at least a portionof human TANGO 265 protein was isolated from a human fetal spleen cDNAlibrary. The human TANGO 265 protein is predicted by structural analysisto be a transmembrane membrane protein, although it can exist in asecreted form as well.

[0780] The full length of the cDNA encoding human TANGO 265 protein(FIG. 27; SEQ ID NO: 387) is 3104 nucleotide residues. The ORF of thiscDNA, nucleotide residues 32 to 2314 of SEQ ID NO: 387 (i.e., SEQ ID NO:388), encodes a 761-amino acid transmembrane protein (FIG. 27; SEQ IDNO: 389).

[0781] The invention thus includes purified TANGO 265 protein, both inthe form of the immature 761 amino acid residue protein (SEQ ID NO: 389)and in the form of the mature 730 amino acid residue protein (SEQ ID NO:391). Mature TANGO 265 protein can be synthesized without the signalsequence polypeptide at the amino terminus thereof, or it can besynthesized by generating immature TANGO 265 protein and cleaving thesignal sequence therefrom.

[0782] The invention includes nucleic acid molecules which encode apolypeptide of the invention. Such nucleic acids include, for example, aDNA molecule having the nucleotide sequence listed in SEQ ID NO: 387 orsome portion thereof, such as the portion which encodes mature TANGO 265protein, immature TANGO 265 protein, or a domain of TANGO 265 protein.These nucleic acids are collectively referred to as nucleic acids of theinvention.

[0783] TANGO 265 proteins and nucleic acid molecules encoding themcomprise a family of molecules having certain conserved structural andfunctional features.

[0784] A common domain present in TANGO 265 proteins is a signalsequence. In one embodiment, a TANGO 265 protein contains a signalsequence corresponding to amino acid residues 1 to 31 of SEQ ID NO: 389(SEQ ID NO: 390). The signal sequence is cleaved during processing ofthe mature protein.

[0785] TANGO 265 proteins can also include an extracellular domain. Thehuman TANGO 265 protein extracellular domain is located from about aminoacid residue 32 to about amino acid residue 683 of SEQ ID NO: 389. TANGO265 can alternately exist in a secreted form, such as a mature proteinhaving the amino acid sequence of amino acid residues 32 to 761 orresidues 32 to about 683 of SEQ ID NO: 389.

[0786] TANGO 265 proteins can also include a transmembrane domain. Inone embodiment, a TANGO 265 protein of the invention contains atransmembrane domain corresponding to about amino acid residues 684 to704 of SEQ ID NO: 389 (SEQ ID NO: 393).

[0787] In addition, TANGO 265 proteins include a cytoplasmic domain,particularly including proteins having a carboxyl-terminal cytoplasmicdomain. The human TANGO 265 cytoplasmic domain is located from aboutamino acid residue 705 to amino acid residue 761 of SEQ ID NO: 389 (SEQID NO: 394).

[0788] TANGO 265 proteins typically comprise a variety of potentialpost-translational modification sites (often within an extracellulardomain), such as those described herein in Table XXIX, as predicted bycomputerized sequence analysis of TANGO 265 proteins using amino acidsequence comparison software (comparing the amino acid sequence of TANGO265 with the information in the PROSITE database {rel. 12.2; February1995} and the Hidden Markov Models database {Rel. PFAM 3.3}). In certainembodiments, a protein of the invention has at least 1, 2, 4, 6, 10, 15,or 20 or more of the post-translational modification sites listed inTable XXIX. TABLE XXIX Type of Potential Modification Site Amino AcidResidues Amino Acid or Domain of SEQ ID NO: 389 Sequence N-glycosylationsite 120 to 123 NETQ 135 to 138 NVTH 496 to 499 NCSV 607 to 610 NGLSGlycosaminoglycan attachment site 70 to 73 SGDG cAMP- or cGMP-dependent108 to 111 RKKS protein kinase phosphorylation site 116 to 119 KKKS 281to 284 KKWT Protein kinase C phosphorylation 106 to 108 SDR site 262 to264 TSR 361 to 363 TSR 366 to 368 TYR 385 to 387 SDK 533 to 535 SWK 555to 557 SLR 721 to 723 TLR 738 to 740 SPK Casein kinase IIphosphorylation 152 to 155 TFIE site 176 to 179 SPFD 250 to 253 TASE 342to 345 SLLD 411 to 414 SGVE 498 to 501 SVYE 502 to 505 SCVD 574 to 577SILE 738 to 741 SPKE 745 to 748 SASD N-myristoylation site 79 to 84GAREAI 191 to 196 GMLYSG 331 to 336 GGTRSS 412 to 417 GVEYTR 437 to 442GTTTGS 620 to 625 GLYQCW 671 to 676 GAALAA Sema domain  64 to 478 SeeFIG. 27

[0789] An example of a domain which occurs in TANGO 265 proteins is asema domain. In one embodiment, the protein of the invention has atleast one domain that is at least 55%, preferably at least about 65%,more preferably at least about 75%, yet more preferably at least about85%, and most preferably at least about 95% identical to one of the semadomains described herein in Table XXIX.

[0790] Sema domains occur in semaphorin proteins. Semaphorins are alarge family of secreted and transmembrane proteins, some of whichfunction as repellent signals during neural axon guidance. The semadomain and a variety of semaphorin proteins in which it occurs aredescribed, for example, in Winberg et al. (1998 Cell 95:903-916). Semadomains also occur in human hepatocyte growth factor receptor (SwissprotAccession no. P08581) and the similar neuronal and epithelialtransmembrane receptor protein (Swissprot Accession no. P51805). Thepresence of an sema domain in human TANGO 265 protein indicates thatTANGO 265 is involved in one or more physiological processes in whichthe semaphorins are involved, has biological activity in common with oneor more of the semaphorins, or both.

[0791] Human TANGO 265 protein exhibits considerable sequence similarityto murine semaphorin B protein (GenBank Accession no. X85991), asindicated herein in FIGS. 27F to 27H. FIGS. 27F to 27H depict analignment of the amino acid sequences of human TANGO 265 protein (SEQ IDNO: 389) and murine semaphorin B protein (SEQ ID NO: 446). In thisalignment (pam120.mat scoring matrix, gap penalties −12/−4), the aminoacid sequences of the proteins are 82.3% identical. FIGS. 271 through27T depict an alignment of the nucleotide sequences of cDNA encodinghuman TANGO 265 protein (SEQ ID NO: 387) and murine cDNA encodingsemaphorin B protein (SEQ ID NO: 447). In this alignment (pamI20.matscoring matrix, gap penalties −12/−4), the nucleic acid sequences of thecDNAs are 76.2% identical. Thus, TANGO 265 is the human orthologue ofmurine semaphorin B and shares functional similarities to that protein.

[0792] It is known that semaphorins are bi-functional, capable offunctioning either as attractive axonal guidance proteins or asrepellent axonal guidance proteins (Wong et al. (1997) Development124:3597-3607). Furthermore, semaphorins bind with neuronal cell surfaceproteins designated plexins, which are expressed on both neuronal cellsand cells of the immune system (Comeau et al. (1998) Immunity 8:473-482;Jin and Strittmatter (1997) J. Neurosci. 17:6256-6263).

[0793] The signal peptide prediction program SIGNALP (Nielsen et al.(1997) Protein Engineering 10:1-6) predicted that human TANGO 265protein includes a 31 amino acid signal peptide (amino acid residues 1to 31 of SEQ ID NO: 389; SEQ ID NO: 390) preceding the mature TANGO 265protein (amino acid residues 32 to 761 of SEQ ID NO: 389; SEQ ID NO:391). Human TANGO 265 protein includes an extracellular domain (aminoacid residues 32 to 683 of SEQ ID NO:389; SEQ ID NO: 392); atransmembrane domain (amino acid residues 684 to 704 of SEQ ID NO: 389;SEQ ID NO: 393); and a cytoplasmic domain (amino acid residues 705 to761 of SEQ ID NO: 389; SEQ ID NO: 394).

[0794]FIG. 27U depicts a hydrophobicity plot of human TANGO 265 protein.Relatively hydrophobic regions are above the dashed horizontal line, andrelatively hydrophilic regions are below the dashed horizontal line. Thehydrophobic region which corresponds to amino acid residues 1 to 31 ofSEQ ID NO: 389 is the signal sequence of human TANGO 265 (SEQ ID NO:390). The hydrophobic region which corresponds to amino acid residues684 to 704 of SEQ ID NO: 389 is the transmembrane domain of human TANGO265 (SEQ ID NO: 393). As described elsewhere herein, relativelyhydrophilic regions are generally located at or near the surface of aprotein, and are more frequently effective immunogenic epitopes than arerelatively hydrophobic regions. For example, the region of human TANGO265 protein from about amino acid residue 350 to about amino acidresidue 375 appears to be located at or near the surface of the protein,while the region from about amino acid residue 230 to about amino acidresidue 250 appears not to be located at or near the surface.

[0795] The predicted molecular weight of human TANGO 265 protein withoutmodification and prior to cleavage of the signal sequence is about 83.6kilodaltons. The predicted molecular weight of the mature human TANGO265 protein without modification and after cleavage of the signalsequence is about 80.2 kilodaltons.

[0796] Chromosomal mapping was performed by computerized comparison ofTANGO 265 cDNA sequences against a chromosomal mapping database in orderto identify the approximate location of the gene encoding human TANGO265 protein. This analysis indicated that the gene was located onchromosome 1 between markers D1 S305 and D1 S2635.

[0797] Uses of TANGO 265 Nucleic Acids,

[0798] Polypeptides, and Modulators Thereof

[0799] TANGO 265 proteins are involved in disorders which affect bothtissues in which they are normally expressed and tissues in which theyare normally not expressed. Based on the observation that TANGO 265 isexpressed in human fetal spleen, involvement of TANGO 265 protein inimmune system development and modulation is indicated.

[0800] The presence of the sema domain in TANGO 265 indicates that thisprotein is involved in development of neuronal and epithelial tissuesand also functions as a repellant protein which guides axonaldevelopment. TANGO 265 modulates nerve growth and regeneration and alsomodulates growth and regeneration of other epithelial tissues.

[0801] TANGO 265 nucleic acids, proteins, and modulators thereof can beused to modulate proliferation, migration, morphology, differentiation,function, or some combination of these, of cells that form the spleen,(e.g., cells of the splenic connective tissue, splenic smooth musclecells, or endothelial cells of the splenic blood vessels) or of bloodcells that are processed (e.g., regenerated, matured, or phagocytized)within the spleen, as described elsewhere in this disclosure.

[0802] The observation that TANGO 265 shares significant identity withmurine semaphorin B suggests that it has activity identical or analogousto the activity of this protein. These observations indicate that TANGO265 modulates growth, proliferation, survival, differentiation, andactivity of neuronal cells and immune system cells. Thus, TANGO 265protein is useful, for example, for guiding neural axon development, formodulating differentiation of cells of the immune system, for modulatingcytokine production by cells of the immune system, for modulatingreactivity of cells of the immune system toward cytokines, formodulating initiation and persistence of an inflammatory response, andfor modulating proliferation of epithelial cells.

[0803] TANGO 286

[0804] A cDNA clone (designated jthkf042e03) encoding at least a portionof human TANGO 286 protein was isolated from a human keratinocyte cDNAlibrary. The human TANGO 286 protein is predicted by structural analysisto be a secreted protein.

[0805] The full length of the cDNA encoding TANGO 286 protein (FIG. 28;SEQ ID NO: 403) is 1980 nucleotide residues. The ORF of this cDNA,nucleotide residues 133 to 1497 of SEQ ID NO: 403 (i.e., SEQ ID NO:404), encodes a 455-amino acid secreted protein (FIG. 28; SEQ ID NO:405).

[0806] The invention thus includes purified TANGO 286 protein, both inthe form of the immature 455 amino acid residue protein (SEQ ID NO: 405)and in the form of the mature 432 amino acid residue protein (SEQ ID NO:407). Mature TANGO 286 protein can be synthesized without the signalsequence polypeptide at the amino terminus thereof, or it can besynthesized by generating immature TANGO 286 protein and cleaving thesignal sequence therefrom.

[0807] The invention includes nucleic acid molecules which encode apolypeptide of the invention. Such nucleic acids include, for example, aDNA molecule having the nucleotide sequence listed in SEQ ID NO: 403 orsome portion thereof, such as the portion which encodes mature TANGO 286protein, immature TANGO 286 protein, or a domain of TANGO 286 protein.These nucleic acids are collectively referred to as nucleic acids of theinvention.

[0808] TANGO 286 proteins and nucleic acid molecules encoding themcomprise a family of molecules having certain conserved structural andfunctional features.

[0809] A common domain of TANGO 286 proteins is a signal sequence. Inone embodiment, a TANGO 286 protein contains a signal sequencecorresponding to amino acid residues 1 to 23 of SEQ ID NO: 405 (SEQ IDNO: 406). The signal sequence is cleaved during processing of the matureprotein.

[0810] TANGO 286 is a secreted soluble protein (i.e., a secreted proteinhaving a single extracellular domain), as indicated by computerizedsequence analysis and comparison of the amino acid sequence of TANGO 286with related proteins, such as the soluble proteins designatedbactericidal permeability increasing (BPI) protein and recombinantendotoxin neutralizing polypeptide (RENP).

[0811] TANGO 286 proteins typically comprise a variety of potentialpost-translational modification sites (often within an extracellulardomain), such as those described herein in Table XXX, as predicted bycomputerized sequence analysis of TANGO 286 proteins using amino acidsequence comparison software (comparing the amino acid sequence of TANGO286 with the information in the PROSITE database {rel. 12.2; February1995} and the Hidden Markov Models database {Rel. PFAM 3.3}). In certainembodiments, a protein of the invention has at least 1, 2, 4, 6, 10, 15,or 20 or more of the post-translational modification sites listed inTable XXX. TABLE XXX Type of Potential Modification Site Amino AcidResidues Amino Acid or Domain of SEQ ID NO: 405 Sequence N-glycosylationsite 79 to 82 NFSN 92 to 95 NTSL 113 to 116 NIST 161 to 164 NLST 173 to176 NYTL 205 to 208 NLTD 249 to 252 NLTL 303 to 306 NFTL 320 to 323 NSTV363 to 366 NRSN Protein kinase C phosphorylation 35 to 37 TQR site 362to 364 SNR 429 to 431 SSK Casein kinase II phosphorylation 63 to 66 SGSEsite 130 to 133 SFAE 163 to 166 STLE 169 to 172 TKID 175 to 178 TLLD 183to 186 SSPE 253 to 256 STEE 321 to 324 STVE 365 to 368 SNIE 409 to 412SDIE N-myristoylation site 42 to 47 GVQAGM 269 to 274 GNVLSRLipid-binding serum glycoprotein  12 to 427 see FIG. 28 domain

[0812] Certain lipid-binding serum glycoproteins, such as LPS-bindingprotein (LBP), bactericidal permeability-increasing protein (BPI),cholesteryl ester transfer protein (CETP), and phospholipid transferprotein (PLTP), share regions of sequence similarity which are hereindesignated a lipid-binding serum glycoprotein domain (Schumann et al.,(1990) Science 249:1429-1431; Gray et al., (1989) J. Biol. Chem.264:9505-9509; Day et al., (1994) J. Biol. Chem. 269:9388-9391). Theconsensus pattern of lipid-binding serum glycoprotein domains is asfollows (using standard single letter amino acid abbreviations wherein Xis any amino acid residue).

[0813] -(P or A)-(G or A)-(L or I or V or M or C)—X₂—R—(I or V)—(S orT)—X₃-L-X(₄ or 5)-(E or Q)-X4-(L or I or V or M)-X(O or I)-(E or Q orK)-X₈—P—(SEQ ID NO: 457; e.g., amino acid residues 28-60 of SEQ ID NO:405).

[0814] Proteins in which a lipid-binding serum glycoprotein domainoccurs are often structurally related and exhibit related physiologicalactivities. LBP binds to lipid A moieties of bacterial LPS and, oncebound thereto, induces secretion of α-tumor necrosis factor, apparentlyby interacting with the CD14 receptor. BPI also binds LPS and exerts acytotoxic effect on Gram-negative bacteria (Elsbach, (1998) J. Leukoc.Biol. 64:14-18). CETP is involved in transfer of insoluble cholesterylesters during reverse cholesterol transport. PLTP appears to be involvedin phospholipid transport and modulation of serum HDL particles.

[0815] The signal peptide prediction program SIGNALP (Nielsen et al.(1997) Protein Engineering 10:1-6) predicted that TANGO 286 proteinincludes a 23 amino acid signal peptide (amino acid residues 1 to 23 ofSEQ ID NO: 405; SEQ ID NO: 406) preceding the mature TANGO 286 protein(amino acid residues 24 to 455 of SEQ ID NO: 45; SEQ ID NO: 407). HumanTANGO 286 protein is a secreted soluble protein.

[0816]FIG. 28E depicts a hydrophobicity plot of TANGO 286 protein.Relatively hydrophobic regions are above the dashed horizontal line, andrelatively hydrophilic regions are below the dashed horizontal line. Asdescribed elsewhere herein, relatively hydrophilic regions are generallylocated at or near the surface of a protein, and are more frequentlyeffective immunogenic epitopes than are relatively hydrophobic regions.For example, the region of human TANGO 286 protein from about amino acidresidue 420 to about amino acid residue 435 appears to be located at ornear the surface of the protein, while the region from about amino acidresidue 325 to about amino acid residue 345 appears not to be located ator near the surface.

[0817] The predicted molecular weight of TANGO 286 protein withoutmodification and prior to cleavage of the signal sequence is about 50.9kilodaltons. The predicted molecular weight of the mature TANGO 286protein without modification and after cleavage of the signal sequenceis about 48.2 kilodaltons.

[0818] The gene encoding human TANGO 286 protein was determined to belocated on chromosome 22 by comparison of matching genomic clones suchas the clones assigned GenBank Accession numbers W16806 and AL021937.

[0819] A portion of TANGO 286 protein exhibits significant amino acidhomology with a region of the human chromosome region 22q12-13 genomicnucleotide sequence having GenBank Accession number AL021937. Alignmentof a 45 kilobase nucleotide sequence encoding TANGO 286 with AL021937,however, indicated the presence in TANGO 286 of exons which differ fromthose disclosed in L021937 (pam1120.mat scoring matrix; gap penalties−12/−4). This region of chromosome 22 comprises an immunoglobulin lambdachain C (IGLC) pseudogene, the Ret finger protein-like 3 (RFPL3) and Retfinger protein-like 3 antisense (RFPL3S) genes, a gene encoding a novelimmunoglobulin lambda chain V family protein, a novel gene encoding aprotein similar both to mouse RGDS protein (RALGDS, RALGEF, guaninenucleotide dissociation stimulator A) and to rabbit oncogene RSC, anovel gene encoding the human orthologue of worm F16A 11.2 protein, anovel gene encoding a protein similar both to BPI and to rabbitliposaccharide-binding protein, and a 5′-portion of a novel gene. Thisregion also comprises various ESTs, STSs, GSSs, genomic marker D22S1175, a ca repeat polymorphism and putative CpG islands. TANGO 286protein thus shares one or more structural or functional features ofthese molecules.

[0820] TANGO 286 protein exhibits considerable sequence similarity withBPI protein, having 23.9% amino acid sequence identity therewith, asassessed using the ALIGN v. 2.0 computer software using a pam120.matscoring matrix and gap penalties of −12/−4. TANGO 286 protein alsoexhibits considerable sequence similarity with recombinant endotoxinneutralizing polypeptide (RENP), having 24.5% amino acid sequenceidentity therewith, as assessed using the ALIGN software. Physiologicalactivities of BPI protein and RENP have been described (e.g., Gabay etal., (1989) Proc. Natl. Acad. Sci. USA 86:5610-5614; Elsbach, (1998) J.Leukoc. Biol. 64:14-18; Mahadeva et al., (1997) Chest 112:1699-1701;International patent application W096/34873). RENP, for example, bindsLPS and neutralizes bacterial endotoxins. BPI, RENP, and other proteinsin which a lipid-binding serum glycoprotein domain occurs bind LPS andneutralize bacterial endotoxins, and are therefore useful forpreventing, detecting, and treating LPS-related disorders such as shock,disseminated intravascular coagulation, anemia, thrombocytopenia, adultrespiratory distress syndrome, renal failure, liver disease, anddisorders associated with Gram negative bacterial infections. Inaddition to the physiological conditions described above, BPI protein isknown to be involved in vasculitis and bronchiectasis, in thatantibodies which bind specifically with BPI protein are present in atleast some patients afflicted with these disorders (Mahadeva et al.,supra).

[0821] Uses of TANGO 286 Nucleic Acids,

[0822] Polypeptides, and Modulators Thereof

[0823] Expression of TANGO 286 in keratinocyte library indicates thatthis protein is involved in a disorders which involve keratinocytes.Such disorders include, for example, disorders involving extracellularmatrix abnormalities, dermatological disorders, ocular disorders,inappropriate hair growth (e.g., baldness), infections of the nails ofthe fingers and toes, scalp disorders (e.g., dandruff), and the like.

[0824] The fact that TANGO 286 protein contains a lipid-binding serumglycoprotein domain indicates that TANGO 286 is involved in one or morephysiological processes in which these other lipid-binding serumglycoprotein domain-containing proteins are involved. Thus, TANGO 286 isinvolved in one or more of lipid transport, metabolism, serum lipidparticle regulation, host anti-microbial defensive mechanisms, and thelike.

[0825] Human TANGO 286 shares physiological functionality with otherproteins in which a lipid-binding serum glycoprotein domains occurs(e.g., LBP, BPI protein, CETP, and PLTP).

[0826] Based on the amino acid sequence similarity of TANGO 286 with BPIprotein and with RENP, TANGO 286 protein exhibits physiologicalactivities exhibited by these proteins. Thus, TANGO 286 proteins areuseful for preventing, diagnosing, and treating, among others, lipidtransport disorders, lipid metabolism disorders, disorders of serumlipid particle regulation, obesity, disorders involving insufficient orinappropriate host anti-microbial defensive mechanisms, vasculitis,bronchiectasis, LPS-related disorders such as shock, disseminatedintravascular coagulation, anemia, thrombocytopenia, adult respiratorydistress syndrome, renal failure, liver disease, and disordersassociated with Gram negative bacterial infections, such as bacteremia,endotoxemia, sepsis, and the like.

[0827] TANGO 294

[0828] A cDNA clone (designated jthrc145g07) encoding at least a portionof human TANGO 294 protein was isolated from a human pulmonary arterysmooth muscle cell cDNA library. The human TANGO 294 protein ispredicted by structural analysis to be a transmembrane membrane protein.No expression of DNA encoding TANGO 294 was detected in human heart,brain, placenta, lung, liver, skeletal muscle, kidney, or pancreastissues.

[0829] The full length of the cDNA encoding TANGO 294 protein (FIG. 29;SEQ ID NO: 415) is 2044 nucleotide residues. The ORF of this cDNA,nucleotide residues 126 to 1394 of SEQ ID NO: 415 (i.e., SEQ ID NO:416), encodes a 423-amino acid transmembrane protein (FIG. 29; SEQ IDNO: 417).

[0830] The invention includes purified TANGO 294 protein, both in theform of the immature 423 amino acid residue protein (SEQ ID NO: 417) andin the form of the mature 390 amino acid residue protein (SEQ ID NO:419). Mature TANGO 294 protein can be synthesized without the signalsequence polypeptide at the amino terminus thereof, or it can besynthesized by generating immature TANGO 294 protein and cleaving thesignal sequence therefrom.

[0831] The invention includes nucleic acid molecules which encode apolypeptide of the invention. Such nucleic acids include, for example, aDNA molecule having the nucleotide sequence listed in SEQ ID NO: 415 orsome portion thereof, such as the portion which encodes mature TANGO 294protein, immature TANGO 294 protein, or a domain of TANGO 294 protein.These nucleic acids are collectively referred to as nucleic acids of theinvention.

[0832] TANGO 294 proteins and nucleic acid molecules encoding themcomprise a family of molecules having certain conserved structural andfunctional features.

[0833] Also included within the scope of the invention are TANGO 294proteins having a signal sequence. In one embodiment, a TANGO 294protein contains a signal sequence corresponding to amino acid residues1 to 33 of SEQ ID NO: 417 (SEQ ID NO: 418). The signal sequence iscleaved during processing of the mature protein.

[0834] The naturally-occurring form of TANGO 294 protein is a secretedprotein (i.e., not comprising the predicted signal sequence). However,in variant forms, TANGO 294 proteins can be transmembrane proteins whichinclude an extracellular domain. In this transmembrane variant form, thepredicted TANGO 294 protein extracellular domain is located from aboutamino acid residue 34 to about amino acid residue 254 of SEQ ID NO: 417,the predicted cytoplasmic domain is located from about amino acidresidue 280 to amino acid residue 423 of SEQ ID NO: 417 (SEQ ID NO:422), and the predicted transmembrane domain is located from about aminoacid residues 255 to 279 of SEQ ID NO: 417 (SEQ ID NO: 421).

[0835] TANGO 294 proteins typically comprise a variety of potentialpost-translational modification sites (often within an extracellulardomain), such as those described herein in Table XXXI, as predicted bycomputerized sequence analysis of TANGO 294 proteins using amino acidsequence comparison software (comparing the amino acid sequence of TANGO294 with the information in the PROSITE database {rel. 12.2; February1995} and the Hidden Markov Models database {Rel. PFAM 3.3}). In certainembodiments, a protein of the invention has at least 1, 2, 4, 6, 10, 15,or 20 or more of the post-translational modification sites listed inTable XXXI. TABLE XXXI Type of Potential Modification Site Amino AcidResidues of Amino Acid or Domain SEQ ID NO: 417 Sequence N-glycosylationsite 48 to 51 NISE 113 to 116 NNSL 285 to 288 NMSR 413 to 416 NLSQProtein kinase C 12 to 14 SHR phosphorylation site 138 to 140 SRK 217 to219 TVK Casein kinase II 155 to 158 SYDE phosphorylation site 175 to 178TGQE 198 to 201 TMPE 360 to 363 SNPE Tyrosine kinase 174 to 182KTGQEKIYY phosphorylation site N-myristoylation site  99 to 104 GLVGGA130 to 135 GNSRGN 188 to 193 GTTMGF 277 to 282 GGFNTN Amidation site 240to 243 FGKK Lipase serine active site 180 to 189 IYYVGYSQGT Alpha/betahydrolase 125 to 404 See FIG. 29 fold domain

[0836] Alpha/beta hydrolase fold domains occur in a wide variety ofenzymes (Ollis et al., (1992) Protein Eng. 5:197-211). The alpha/betafold domain is a conserved topological domain in which sequence homologyis not necessarily conserved. Conservation of topology in the alpha/betafold domain preserves arrangement of catalytic residues, even thoughthose residues, and the reactions they catalyze, can vary. In manyenzymes, particularly including alpha/beta hydrolases, this domainencompasses the active site of the enzyme. In one embodiment, theprotein of the invention has at least one domain that is at least 55%,preferably at least about 65%, more preferably at least about 75%, yetmore preferably at least about 85%, and most preferably at least about95% identical to the alpha/beta hydrolase fold domain described hereinin Table XXXI.

[0837] The signal peptide prediction program SIGNALP (Nielsen et al.(1997) Protein Engineering 10:1-6) predicted that human TANGO 294protein includes a 33 amino acid signal peptide (amino acid residues 1to 33 of SEQ ID NO: 417; SEQ ID NO: 418) preceding the mature TANGO 294protein (amino acid residues 34 to 423 of SEQ ID NO: 417; SEQ ID NO:419). Human TANGO 294 protein is a soluble secreted protein. However, inthe transmembrane variant form, human TANGO 294 protein includes anextracellular domain (amino acid residues 34 to 254 of SEQ ID NO: 417;SEQ ID NO: 420); a transmembrane domain (amino acid residues 255 to 279of SEQ ID NO: 417; SEQ ID NO: 421); and a cytoplasmic domain (amino acidresidues 280 to 423 of SEQ ID NO: 417; SEQ ID NO: 422).

[0838]FIG. 29F depicts a hydrophobicity plot of human TANGO 294 protein.Relatively hydrophobic regions are above the dashed horizontal line, andrelatively hydrophilic regions are below the dashed horizontal line. Thehydrophobic region which corresponds to amino acid residues 1 to 33 ofSEQ ID NO: 417 is the signal sequence of human TANGO 294 (SEQ ID NO:419). The hydrophobic region which corresponds to amino acid residues255 to 279 of SEQ ID NO: 417 is the predicted transmembrane domain ofhuman TANGO 294 (SEQ ID NO: 421). As described elsewhere herein,relatively hydrophilic regions are generally located at or near thesurface of a protein, and are more frequently effective immunogenicepitopes than are relatively hydrophobic regions. For example, theregion of human TANGO 294 protein from about amino acid residue 130 toabout amino acid residue 150 appears to be located at or near thesurface of the protein, while the region from about amino acid residue90 to about amino acid residue 100 appears not to be located at or nearthe surface.

[0839] The predicted molecular weight of human TANGO 294 protein withoutmodification and prior to cleavage of the signal sequence is about 48.2kilodaltons. The predicted molecular weight of the mature human TANGO294 protein without modification and after cleavage of the signalsequence is about 44.2 kilodaltons.

[0840] It may be that amino acid residues 1 to 15 of SEQ ID NO: 417 donot occur in TANGO 294 protein. However, it is recognized that aminoacid residues 16 to 33 of SEQ ID NO: 417 form a functional signalsequence even in the absence of residues 1 to 15. The amino acidsequence (and hence the properties) of mature TANGO 294 protein areunaffected by presence or absence of amino acid residues 1 to 15 ofimmature TANGO 294 protein.

[0841] Human TANGO 294 protein exhibits considerable sequence similarity(i.e., about 75% amino acid sequence identity) to lingual and gastriclipase proteins of rat (Swissprot Accession no. PO₄₆₃₄; Docherty et al.(1985) Nucleic Acids Res. 13:1891-1903), dog (Swissprot Accession no.P80035; Carriere et al. (1991) Eur. J. Biochem. 202:75-83), and human(Swissprot Accession no. P07098; Bernbaeck and Blaeckberg (1987)Biochim. Biophys. Acta 909:237-244), as assessed using the ALIGN v. 2.0computer software using a paml2.mat scoring matrix and gap penalties of−12/−4. TANGO 294 is distinct from the known human lipase, as indicatedin FIGS. 29D and 29E. FIGS. 29D and 29E depict an alignment of the aminoacid sequences of human TANGO 294 protein (SEQ ID NO: 417) and the knownhuman lipase protein (SEQ ID NO: 445), as assessed using the samesoftware and parameters. In this alignment (pam120.mat scoring matrix,gap penalties −12/−4), the amino acid sequences of the proteins are49.8% identical. TANGO 294 also is distinct from the known humanlysosomal acid lipase, as indicated in FIGS. 29G and 29H. FIGS. 29G and29H depicts an alignment of the amino acid sequences of human TANGO 294protein (SEQ ID NO: 417) and the known human lysosomal acid lipaseprotein (SEQ ID NO: 411). In this alignment (pam120.mat scoring matrix,gap penalties −12/−4), the amino acid sequences of the proteins are56.9% identical.

[0842] TANGO 294 is a human lipase distinct from the known human lipaseand the known human lysosomal acid lipase. Furthermore, in view of thecomparisons of the amino acid sequences of TANGO 294 and the two humanlipases and the nature of transcriptional initiation sites, it isrecognized that the transcriptional start site can correspond to eitherof the methionine residues located at residues 1 and 15 of SEQ ID NO:417 The present invention thus includes proteins in which the initiallytranscribed amino acid residue is the methionine residue at position Iof SEQ ID NO: 417 and proteins in which the initially transcribed aminoacid residue is the methionine residue at position 15 of SEQ ID NO: 417(i.e., proteins in which the amino acid sequence of TANGO 294 does notinclude residues 1 to 14 of SEQ ID NO: 417). Furthermore, because aminoacid residues 1 to 14 of SEQ ID NO: 417 are predicted to be part of asignal sequence, it is recognized that the protein not comprising thisportion of the amino acid sequence will nonetheless exhibit a functionalsignal sequence at its amino terminus.

[0843] Uses of TANGO 294 Nucleic Acids,

[0844] Polypeptides, and Modulators Thereof

[0845] The sequence similarity of TANGO 294 and mammalian lingual,gastric, and lysosomal acid lipase proteins indicates that TANGO 294 isinvolved in physiological processes identical or analogous to thoseinvolving these lipases. Thus, TANGO 294 is involved in facilitatingabsorption and metabolism of fat. TANGO 294 can thus be used, forexample, to prevent, detect, and treat disorders relating to fatabsorption and metabolism, such as inadequate expression ofgastric/pancreatic lipase, cystic fibrosis, exocrine pancreaticinsufficiency, obesity, medical treatments which alter fat absorption,and the like.

[0846] TANGO 294 protein is known to be expressed in human pulmonaryartery smooth muscle tissue. This indicates that TANGO 294 protein isinvolved in transportation and metabolism of fats and lipids in thehuman vascular and cardiovascular systems. Thus, TANGO 294 proteins ofthe invention can be used to prevent, detect, and treat disordersinvolving these body systems.

[0847] INTERCEPT 296

[0848] A cDNA clone (designated jthEa030h09) encoding at least a portionof human INTERCEPT 296 protein was isolated from a human esophagus cDNAlibrary. The human INTERCEPT 296 protein is predicted by structuralanalysis to be a transmembrane protein having three or moretransmembrane domains. Expression of DNA encoding INTERCEPT 296 tissuehas been detected by northern analysis of human lung tissue. In humanlung tissue, two moieties corresponding to INTERCEPT 296 have beenidentified in Northern blots. It is recognized that these two moietiesmay represent alternatively polyadenylated INTERCEPT 296 mRNAs oralternatively spliced INTERCEPT 296 mRNAs. It has furthermore beenobserved that INTERCEPT 296 does not appear to be expressed in any ofheart, brain, placenta, skeletal muscle, kidney, and pancreas tissues.

[0849] The full length of the cDNA encoding INTERCEPT 296 protein (FIG.30; SEQ ID NO: 423) is 2133 nucleotide residues. The ORF of this cDNA,nucleotide residues 70 to 1098 of SEQ ID NO: 423 (i.e., SEQ ID NO: 424),encodes a 343-amino acid transmembrane protein (FIG. 30; SEQ ID NO:425).

[0850] The invention includes nucleic acid molecules which encode apolypeptide of the invention. Such nucleic acids include, for example, aDNA molecule having the nucleotide sequence SEQ ID NO: 423 or someportion thereof, such as the portion which encodes INTERCEPT 296 proteinor a domain thereof. These nucleic acids are collectively referred to asnucleic acids of the invention.

[0851] INTERCEPT 296 proteins and nucleic acid molecules encoding themcomprise a family of molecules having certain conserved structural andfunctional features, such as the five transmembrane domains which occurin the protein.

[0852] INTERCEPT 296 comprises at least five transmembrane domains, atleast three cytoplasmic domains, and at least two extracellular domains.INTERCEPT 296 does not appear to comprise a cleavable signal sequence.Amino acid residues 1 to 70 of SEQ ID NO: 425 likely directs insertionof the protein into the cytoplasmic membrane. There are at least twomechanisms by which this can occur. Sequence analysis of residues 1 to70 of SEQ ID NO: 425 indicates that this entire region may represent asignal sequence or that residues 1 to 47 represent a signal sequence,with residues 48-70 representing a transmembrane region. Human INTERCEPT296 protein extracellular domains are located from about amino acidresidue 70 to about amino acid residue 182 (SEQ ID NO: 427) and fromabout amino acid residue 228 to about amino acid residue 249 (SEQ ID NO:428) of SEQ ID NO: 425. Human INTERCEPT 296 cytoplasmic domains arelocated from about amino acid residue 43 to amino acid residue 50 (SEQID NO: 434), from about amino acid residue 205 to amino acid residue 210(SEQ ID NO: 435), and from amino acid residue 272 to amino acid residue343 (SEQ ID NO: 436) of SEQ ID NO: 425. The five transmembrane domainsof INTERCEPT 296 are located from about amino acid residues 24 to 42(SEQ ID NO: 429), 51 to 70 (SEQ ID NO: 430), 183 to 204 (SEQ ID NO:431), 211 to 227 (SEQ ID NO: 432), and 250 to 271 (SEQ ID NO: 433) ofSEQ ID NO: 425.

[0853] INTERCEPT 296 proteins typically comprise a variety of potentialpost-translational modification sites (often within an extracellulardomain), such as those described herein in Table XXXII, as predicted bycomputerized sequence analysis of INTERCEPT 296 proteins using aminoacid sequence comparison software (comparing the amino acid sequence ofINTERCEPT 296 with the information in the PROSITE database {rel. 12.2;February 1995} and the Hidden Markov Models database {Rel. PFAM 3.3}).In certain embodiments, a protein of the invention has at least 1, 2, 4,6, 10, 15, or 20 or more of the post-translational modification siteslisted in Table XXXII. TABLE XXXII Type of Potential Modification AminoAcid Residues Amino Acid Site or Domain of SEQ ID NO: 425 SequenceN-glycosylation site 71 to 74 NFSS 84 to 87 NTSY 109 to 112 NITL 121 to124 NETI 284 to 287 NQSV Protein kinase C 86 to 88 SYK phosphorylationsite 131 to 133 TWR 162 to 164 TPR 304 to 306 SPR 313 to 315 SPK 326 to328 STK Casein kinase II 286 to 289 SVDE phosphorylation site 296 to 299SPEE 309 to 312 SMAD Tyrosine kinase phosphorylation 148 to 156KGLPDPVLY site 79 to 84 GQVSTN N-myristoylation site 100 to 105 GLQVGL107 to 112 GVNITL 265 to 270 GLAMAV

[0854]FIG. 30D depicts a hydrophobicity plot of INTERCEPT 296 protein.Relatively hydrophobic regions are above the dashed horizontal line, andrelatively hydrophilic regions are below the dashed horizontal line. Thehydrophobic regions which corresponds to amino acid residues 24 to 42,51 to 70, 183 to 204, 211 to 227, and 250 to 271 of SEQ ID NO: 425 arethe transmembrane domains of human INTERCEPT 296 (SEQ ID NOs: 429through 433, respectively). As described elsewhere herein, relativelyhydrophilic regions are generally located at or near the surface of aprotein, and are more frequently effective immunogenic epitopes than arerelatively hydrophobic regions. For example, the region of humanINTERCEPT 296 protein from about amino acid residue 120 to about aminoacid residue 140 appears to be located at or near the surface of theprotein, while the region from about amino acid residue 95 to aboutamino acid residue 110 appears not to be located at or near the surface.

[0855] The predicted molecular weight of INTERCEPT 296 protein withoutmodification and prior to cleavage of the signal sequence is about 37.8kilodaltons. The predicted molecular weight of the mature INTERCEPT 296protein without modification and after cleavage of the signal sequenceis about 30.2 kilodaltons.

[0856]FIGS. 30E through 30G depicts an alignment of the amino acidsequences of human INTERCEPT 296 protein (SEQ ID NO: 425) andCaenorhabditis elegans C06E1.3 related protein (SEQ ID NO: 410). In thisalignment (pam120.mat scoring matrix, gap penalties −12/−4), the aminoacid sequences of the proteins are 26.8% identical. The C. elegansprotein has five predicted transmembrane domains.

[0857] Uses of INTERCEPT 296 Nucleic Acids,

[0858] Polypeptides, and Modulators Thereof

[0859] The cDNA encoding INTERCEPT 296 protein was obtained from a humanesophagus cDNA library, and INTERCEPT 296 is expressed in lung tissue.The INTERCEPT 296-related proteins and nucleic acids of the inventionare therefore useful for prevention, detection, and treatment ofdisorders of the human lung and esophagus. Examples of lung disorders inwhich INTERCEPT 296 can be involved include the lung disorders describedelsewhere in this disclosure. Examples of disorders of the esophagus inwhich INTERCEPT 296 can be involved include dysphagia, achalasia,heartburn, symptomatic diffuse esophageal spasm, corrosive esophagitis,candidiasis, and gastroesophageal reflux disease.

[0860] Tables A-1, A-2 and B-I to B-5 summarize sequence datacorresponding to the human nucleic acids and proteins disclosed herein.Tables A-3 and B-6 summarize sequence data corresponding to thenon-human nucleic acids and proteins disclosed herein. TABLE A-1Depicted Protein SEQ ID NOs in ATCC ® Designation cDNA ORF ProteinFigure # Accession # TANGO 416 1 2 3 1 PTA-1764 TANGO416 32 32 33 1PTA-1764 (alt.form) TANGO 457 51 52 53 7 PTA-817 TANGO 229 71 72 73 10PTA-295 INTERCEPT 289 PTA-295 form 1a 81 82 83 11 form 1b 91 92 93 11form 2a 96 97 98 11 form 2b 101 102 103 11 form 3a 106 107 108 11 form3b 111 112 113 11 INTERCEPT 309 121 122 123 12 PTA-1156 MANGO 419 141142 143 13 PTA-1156 INTERCEPT 429 151 152 153 14 PTA-455 TANGO 210 171172 173 15 PTA-438 TANGO 366 191 192 193 16 PTA-424 INTERCEPT 394 201202 203 17 PTA-424 INTERCEPT 400 221 222 223 18 PTA-438 INTERCEPT 217271 272 273 19 PTA-147 INTERCEPT 297 279 280 281 20 PTA-147 TANGO 276303 304 305 21 PTA-150 TANGO 292 308 309 310 22 207230 TANGO 331 324 325326 23 PTA-147

[0861] TABLE A-2 Depicted Protein SEQ ID NOs in ATCC ® Designation cDNAORF Protein Figure # Accession # TANGO 332 329 330 331 24 PTA-151 TANGO202 371 372 373 25 207219 TANGO 234 379 380 381 26 207184 TANGO 265 387388 389 27 207228 TANGO 286 403 404 405 28 207220 TANGO 294 415 416 41729 207220 INTERCEPT 296 423 424 425 30 207220

[0862] TABLE A-3 Protein SEQ ID NOs Depicted in ATCC ® Designation cDNAORF Protein Figure # Accession # murine 161 162 163 11 INTERCEPT 289murine 181 182 183 15 TANGO 210 murine 241 242 243 18 INTERCEPT 400 rat251 252 253 18 INTERCEPT 400 murine 362 363 19 INTERCEPT 217 gerbil 351352 353 22 TANGO 292 murine 437 438 439 25 TANGO 202

[0863] TABLE B-1

[0864] TABLE B-2

[0865] TABLE B-3

[0866] TABLE B-4

[0867] TABLE B-5

[0868] TABLE B-6

[0869] Various aspects of the invention are described in further detailin the following subsections.

[0870] I. Isolated Nucleic Acid Molecules

[0871] One aspect of the invention pertains to isolated nucleic acidmolecules that encode a polypeptide of the invention or a biologicallyactive portion thereof, as well as nucleic acid molecules sufficient foruse as hybridization probes to identify nucleic acid molecules encodinga polypeptide of the invention and fragments of such nucleic acidmolecules suitable for use as PCR primers for the amplification ormutation of nucleic acid molecules.

[0872] As used herein, the term “nucleic acid molecule” is intended toinclude DNA molecules (e.g., cDNA or genomic DNA) and RNA molecules(e.g., mRNA) and analogs of the DNA or RNA generated using nucleotideanalogs. The nucleic acid molecule can be single-stranded ordouble-stranded. An “isolated” nucleic acid molecule is one which isseparated from other nucleic acid molecules which are present in thenatural source of the nucleic acid molecule. Preferably, an “isolated”nucleic acid molecule is free of sequences (preferably protein-encodingsequences) which naturally flank the nucleic acid (i.e., sequenceslocated at the 5′ and 3′ ends of the nucleic acid) in the genomic DNA ofthe organism from which the nucleic acid is derived. For example, invarious embodiments, the isolated nucleic acid molecule can contain lessthan about 5, 4, 3, 2, 1, 0.5, or 0.1 kilobases of nucleotide sequenceswhich naturally flank the nucleic acid molecule in genomic DNA of thecell from which the nucleic acid is derived. Moreover, an “isolated”nucleic acid molecule, such as a cDNA molecule, can be substantiallyfree of other cellular material, or culture medium when produced byrecombinant techniques, or substantially free of chemical precursors orother chemicals when chemically synthesized.

[0873] A nucleic acid molecule of the present invention, e.g., a nucleicacid molecule having the nucleotide sequence of all or a portion of anyof SEQ ID NOs: 1, 2, 31, 32, 51, 52, 71, 72, 81, 82, 91, 92, 96, 97,101, 102, 106, 107, 111, 112, 121, 122, 141, 142, 151, 152, 161, 162,171, 172, 181, 182, 191, 192, 201, 202, 215, 217, 221, 222, 241, 242,251, 252, 271, 272, 279, 280, 303, 304, 308, 309, 324, 325, 329, 330,351, 352, 362, 371, 372, 379, 380, 387, 388, 403, 404, 415, 416, 423,424, 437, 438, and the nucleotide sequence of any of the clonesdeposited as ATCC® Accession numbers 207184, 207219, 207220, 207221,207228, 207230, PTA-147, PTA-150, PTA-151, PTA-295, PTA-424, PTA-438,PTA-455, PTA-817, PTA-1156, and PTA-1764, or a complement thereof, orwhich has a nucleotide sequence comprising one of these sequences, canbe isolated using standard molecular biology techniques and the sequenceinformation provided herein. Using all or a portion of the nucleic acidsequences of any of SEQ ID NOs: 1, 2, 31, 32, 51, 52, 71, 72, 81, 82,91, 92, 96, 97, 101, 102, 106, 107, 111, 112, 121, 122, 141, 142, 151,152, 161, 162, 171, 172, 181, 182, 191, 192, 201, 202, 215, 217, 221,222, 241, 242, 251, 252, 271, 272, 279, 280, 303, 304, 308, 309, 324,325, 329, 330, 351, 352, 362, 371, 372, 379, 380, 387, 388, 403, 404,415, 416, 423, 424, 437, 438, and the nucleotide sequence of any of theclones deposited as ATCC® Accession numbers 207184, 207219, 207220,207221, 207228, 207230, PTA-147, PTA-150, PTA-151, PTA-295, PTA-424,PTA-438, PTA-455, PTA-817, PTA-1156, and PTA-1764 as a hybridizationprobe, nucleic acid molecules of the invention can be isolated usingstandard hybridization and cloning techniques (e.g., as described inSambrook et al., Eds., Molecular Cloning: A Laboratory Manual, 2nd ed.,Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, ColdSpring Harbor, N.Y., 1989).

[0874] A nucleic acid molecule of the invention can be amplified usingcDNA, mRNA, or genomic DNA as a template and appropriate oligonucleotideprimers according to standard PCR amplification techniques. The nucleicacid so amplified can be cloned into an appropriate vector andcharacterized by DNA sequence analysis. Furthermore, oligonucleotidescorresponding to all or a portion of a nucleic acid molecule of theinvention can be prepared by standard synthetic techniques, e.g., usingan automated DNA synthesizer.

[0875] In another embodiment, an isolated nucleic acid molecule of theinvention comprises a nucleic acid molecule which is a complement of thenucleotide sequence of any of SEQ ID NOs: 1, 2, 31, 32, 51, 52, 71, 72,81, 82, 91, 92, 96, 97, 101, 102, 106, 107, 111, 112, 121, 122, 141,142, 151, 152, 161, 162, 171, 172, 181, 182, 191, 192, 201, 202, 215,217, 221, 222, 241, 242, 251, 252, 271, 272, 279, 280, 303, 304, 308,309, 324, 325, 329, 330, 351, 352, 362, 371, 372, 379, 380, 387, 388,403, 404, 415, 416, 423, 424, 437, 438, and the nucleotide sequence ofany of the clones deposited as ATCC® Accession numbers 207184, 207219,207220, 207221, 207228, 207230, PTA-147, PTA-150, PTA-151, PTA-295,PTA-424, PTA-438, PTA-455, PTA-817, PTA-1156, and PTA-1764, or a portionthereof. A nucleic acid molecule which is complementary to a givennucleotide sequence is one which is sufficiently complementary to thegiven nucleotide sequence that it can hybridize with the givennucleotide sequence thereby forming a stable duplex.

[0876] Moreover, a nucleic acid molecule of the invention can comprise aportion of a nucleic acid sequence encoding a full length polypeptide ofthe invention, such as a fragment which can be used as a probe or primeror a fragment encoding a biologically active portion of a polypeptide ofthe invention. The nucleotide sequence determined from cloning one geneallows generation of probes and primers designed for identifying and/orcloning homologs in other cell types, e.g., from other tissues, as wellas homologs from other mammals. The probe/primer typically comprisessubstantially purified oligonucleotide. The oligonucleotide typicallycomprises a region of nucleotide sequence that hybridizes understringent conditions with at least about 15, preferably about 25, morepreferably about 40, 60, 80, 100, 150, 200, 250, 300, 350, 400, 450,550, 650, 700, 800, 900, 1000, 1200, 1400, 1410, 1600, 1800, 2000, 2200,2400, 2600, 2800, 3000, 3500, 4000, 4500, or 5000 or more-consecutivenucleotides of the sense or anti-sense sequence of any of SEQ ID NOs: 1,2, 31, 32, 51, 52, 71, 72, 81, 82, 91, 92, 96, 97, 101, 102, 106, 107,111, 112, 121, 122, 141, 142, 151, 152, 161, 162, 171, 172, 181, 182,191, 192, 201, 202, 215, 217, 221, 222, 241, 242, 251, 252, 271, 272,279, 280, 303, 304, 308, 309, 324, 325, 329, 330, 351, 352, 362, 371,372, 379, 380, 387, 388, 403, 404, 415, 416, 423, 424, 437, 438, and thenucleotide sequence of any of the clones deposited as ATCC® Accessionnumbers 207184, 207219, 207220, 207221, 207228, 207230, PTA-147,PTA-150, PTA-151, PTA-295, PTA-424, PTA-438, PTA-455, PTA-817, PTA-1156,and PTA-1764, or of a naturally occurring mutant of any of thesesequences.

[0877] Probes based on the sequence of a nucleic acid molecule of theinvention can be used to detect transcripts or genomic sequencesencoding the same protein molecule encoded by a selected nucleic acidmolecule. The probe comprises a label group attached thereto, e.g., aradioisotope, a fluorescent compound, an enzyme, or an enzyme co-factor.Such probes can be used as part of a diagnostic test kit for identifyingcells or tissues which aberrantly express the protein, such as bymeasuring levels of a nucleic acid molecule encoding the protein in asample of cells from a subject, e.g., detecting mRNA levels ordetermining whether a gene encoding the protein has been mutated ordeleted.

[0878] A nucleic acid fragment encoding a biologically active portion ofa polypeptide of the invention can be prepared by isolating a portion ofone of SEQ ID NOs: 2, 32, 52, 72, 82, 92, 97, 102, 107, 112, 122, 142,152, 162, 172, 182, 192, 202, 215, 222, 242, 252, 272, 280, 304, 309,325, 330, 352, 362, 372, 380, 388, 404, 416, 424, and 438 expressing theencoded portion of the polypeptide protein (e.g., by recombinantexpression in vitro), and assessing the activity of the encoded portionof the polypeptide.

[0879] The invention further encompasses nucleic acid molecules thatdiffer from the nucleotide sequence of any of SEQ ID NOs: 1, 2, 31, 32,51, 52, 71, 72, 81, 82, 91, 92, 96, 97, 101, 102, 106, 107, 111, 112,121, 122, 141, 142, 151, 152, 161, 162, 171, 172, 181, 182, 191, 192,201, 202, 215, 217, 221, 222, 241, 242, 251, 252, 271, 272, 279, 280,303, 304, 308, 309, 324, 325, 329, 330, 351, 352, 362, 371, 372, 379,380, 387, 388, 403, 404, 415, 416, 423, 424, 437, 438, and thenucleotide sequence of any of the clones deposited as ATCC® Accessionnumbers 207184, 207219, 207220, 207221, 207228, 207230, PTA-147,PTA-150, PTA-151, PTA-295, PTA-424, PTA-438, PTA-455, PTA-817, PTA-1156,and PTA-1764, due to degeneracy of the genetic code and thus encode thesame protein as that encoded by the nucleotide sequence of one of SEQ IDNOs: 2, 32, 52, 72, 82, 92, 97, 102, 107, 112, 122, 142, 152, 162, 172,182, 192, 202, 215, 222, 242, 252, 272, 280, 304, 309, 325, 330, 352,362, 372, 380, 388, 404, 416, 424, and 438.

[0880] In addition to the nucleotide sequences of one of SEQ ID NOs: 2,32, 52, 72, 82, 92, 97, 102, 107, 112, 122, 142, 152, 162, 172, 182,192, 202, 215, 222, 242, 252, 272, 280, 304, 309, 325, 330, 352, 362,372, 380, 388, 404, 416, 424, and 438, it will be appreciated by thoseskilled in the art that DNA sequence polymorphisms that lead to changesin the amino acid sequence can exist within a population (e.g., thehuman population). Such genetic polymorphisms can exist amongindividuals within a population due to natural allelic variation. Anallele is one of a group of genes which occur alternatively at a givengenetic locus.

[0881] To determine the percent identity of two amino acid sequences orof two nucleic acids, the sequences are aligned for optimal comparisonpurposes (e.g., gaps can be introduced in the sequence of a first aminoacid or nucleic acid sequence for optimal alignment with a second aminoor nucleic acid sequence). The amino acid residues or nucleotides atcorresponding amino acid positions or nucleotide positions are thencompared. When a position in the first sequence is occupied by the sameamino acid residue or nucleotide as the corresponding position in thesecond sequence, then the molecules are identical at that position. Thepercent identity between the two sequences is a function of the numberof identical positions shared by the sequences (i.e., % identity=# ofidentical positions/total # of positions {e.g., overlappingpositions}×100). In one embodiment, the two sequences are the samelength.

[0882] The determination of percent identity between two sequences canbe accomplished using a mathematical algorithm. A preferred,non-limiting example of a mathematical algorithm utilized for thecomparison of two sequences is the algorithm of Karlin and Altschul(1990) Proc. Natl. Acad. Sci. USA 87:2264-2268, modified as in Karlinand Altschul (1993) Proc. Natl. Acad. Sci. USA 90:5873-5877. Such analgorithm is incorporated into the NBLAST and XBLAST programs ofAltschul, et al. (1990) J. Mol. Biol. 215:403-410. BLAST nucleotidesearches can be performed with the NBLAST program, score=100,wordlength=12 to obtain nucleotide sequences homologous to a nucleicacid molecules of the invention.

[0883] BLAST protein searches can be performed with the XBLAST program,score=50, wordlength=3 to obtain amino acid sequences homologous to aprotein molecules of the invention. To obtain gapped alignments forcomparison purposes, Gapped BLAST can be utilized as described inAltschul et al. (1997) Nucleic Acids Res. 25:3389-3402. Alternatively,PSI-Blast can be used to perform an iterated search which detectsdistant relationships between molecules (Id.). When utilizing BLAST,Gapped BLAST, and PSI-Blast programs, the default parameters of therespective programs (e.g., XBLAST and NBLAST) can be used. Seehttp://www.ncbi.nlm.nih.gov.

[0884] Another preferred, non-limiting example of a mathematicalalgorithm utilized for the comparison of sequences is the local homologyalgorithm of Smith and Waterman (Advances in Applied Mathematics 2:482-489 (1981)). Such an algorithm is incorporated into the BestFitprogram, which is part of the Wisconsin™ package, and is used to findthe best segment of similarity between two sequences. BestFit reads ascoring matrix that contains values for every possible GCG symbol match.The program uses these values to construct a path matrix that representsthe entire surface of comparison with a score at every position for thebest possible alignment to that point. The quality score for the bestalignment to any point is equal to the sum of the scoring matrix valuesof the matches in that alignment, less the gap creation penaltymultiplied by the number of gaps in that alignment, less the gapextension penalty multiplied by the total length of all gaps in thatalignment. The gap creation and gap extension penalties are set by theuser. If the best path to any point has a negative value, a zero is putin that position.

[0885] After the path matrix is complete, the highest value on thesurface of comparison represents the end of the best region ofsimilarity between the sequences. The best path from this highest valuebackwards to the point where the values revert to zero is the alignmentshown by BestFit. This alignment is the best segment of similaritybetween the two sequences. Further documentation can be found athttp://ir.ucdavis.edu/GCGhelp/bestfit.html#algorithm.

[0886] Additional algorithms for sequence analysis are known in the artand include ADVANCE and ADAM as described in Torellis and Robotti (1994)Comput. Appl. Biosci., 10:3-5; and FASTA described in Pearson and Lipman(1988) Proc. Natl. Acad. Sci. 85:2444-8. Within FASTA, ktup is a controloption that sets the sensitivity and speed of the search. If ktup=2,similar regions in the two sequences being compared are found by lookingat pairs of aligned residues; if ktup=1, single aligned amino acids areexamined. ktup can be set to 2 or 1 for protein sequences, or from 1 to6 for DNA sequences. The default if ktup is not specified is 2 forproteins and 6 for DNA. For a further description of FASTA parameters,see http://bioweb.pasteur.fr/docs/man/man/fasta.1.html#sect2, thecontents of which are incorporated herein by reference.

[0887] The percent identity between two sequences can be determinedusing techniques similar to those described above, with or withoutallowing gaps. In calculating percent identity, typically exact matchesare counted.

[0888] As used herein, the phrase “allelic variant” refers to anucleotide sequence which occurs at a given locus or to a polypeptideencoded by the nucleotide sequence. For example, the TANGO 457 geneexhibits significant homology with a portion of human chromosome 11p14.3PAC present in a clone designated pDJ239b22 and having GENBANK™accession number AC003969; the TANGO 416 gene exhibits significanthomology with a portion of chromosome 4 between chromosomal markersD4S422 and D4S 1576; the INTERCEPT 400 gene exhibits significanthomology with a portion of chromosome 4 between markers D4S1616 andD4S1611; the TANGO 331 gene exhibits significant homology with a portionof chromosome 22 at 22q13-q13, between markers WI-4572 and WI-8917; theTANGO 265 gene exhibits significant homology with a portion ofchromosome 1 between markers D1S305 and D1S2635; and the TANGO 286 geneexhibits significant homology with a portion of chromosome 22 at22q12-13. Allelic variants of any of these genes can be identified bysequencing the corresponding chromosomal portion at the indicatedlocation in multiple individuals.

[0889] As used herein, the terms “gene” and “recombinant gene” refer tonucleic acid molecules comprising an open reading frame encoding apolypeptide of the invention. Such natural allelic variations cantypically result in 1-5% variance in the nucleotide sequence of a givengene. Alternative alleles can be identified by sequencing the gene ofinterest in a number of different individuals. This can be readilycarried out by using hybridization probes to identify the same geneticlocus in a variety of individuals. Any and all such nucleotidevariations and resulting amino acid polymorphisms or variations that arethe result of natural allelic variation and that do not alter thefunctional activity are intended to be within the scope of theinvention.

[0890] Moreover, nucleic acid molecules encoding proteins of theinvention from other species (homologs), which have a nucleotidesequence which differs from that of the human proteins described hereinare within the scope of the invention. Nucleic acid moleculescorresponding to natural allelic variants and homologs of a cDNA of theinvention can be isolated based on their identity to human nucleic acidmolecules using the human cDNAs, or a portion thereof, as ahybridization probe according to standard hybridization techniques understringent hybridization conditions. For example, a cDNA encoding asoluble form of a membrane-bound protein of the invention can beisolated based on its hybridization with a nucleic acid moleculeencoding all or part of the membrane-bound form. Likewise, a cDNAencoding a membrane-bound form can be isolated based on itshybridization with a nucleic acid molecule encoding all or part of thesoluble form.

[0891] Accordingly, in another embodiment, an isolated nucleic acidmolecule of the invention is at least 15 (25, 40, 60, 80, 100, 150, 200,250, 300, 350, 400, 450, 500, 600, 700, 800, 900, 1000, 1200, 1400,1600, 1800, 2000, 2200, 2400, 2600, 2800, 3000, 3500, 4000, 4500, 5000,or more) nucleotides in length and hybridizes under stringent conditionsto the nucleic acid molecule comprising the nucleotide sequence,preferably the coding sequence, of any of SEQ ID NOs: 1, 2, 31, 32, 51,52, 71, 72, 81, 82, 91, 92, 96, 97, 101, 102, 106, 107, 111, 112, 121,122, 141, 142, 151, 152, 161, 162, 171, 172, 181, 182, 191, 192, 201,202, 215, 217, 221, 222, 241, 242, 251, 252, 271, 272, 279, 280, 303,304, 308, 309, 324, 325, 329, 330, 351, 352, 362, 371, 372, 379, 380,387, 388, 403, 404, 415, 416, 423, 424, 437, 438, and the nucleotidesequence of any of the clones deposited as ATCC® Accession numbers207184, 207219, 207220, 207221, 207228, 207230, PTA-147, PTA-150,PTA-151, PTA-295, PTA-424, PTA-438, PTA-455, PTA-817, PTA-1156, andPTA-1764, or a complement thereof. As used herein, the term “hybridizesunder stringent conditions” is intended to describe conditions forhybridization and washing under which nucleotide sequences at least 60%(65%, 70%, preferably 75%) identical to each other typically remainhybridized with each other. Such stringent conditions are known to thoseskilled in the art and can be found in Current Protocols in MolecularBiology, John Wiley & Sons, N.Y. (1989), 6.3.1-6.3.6. A example ofstringent hybridization conditions are hybridization in 6× sodiumchloride/sodium citrate (SSC) at about 45° C., followed by one or morewashes in 0.2×SSC, 0.1% SDS at 50-65° C. Preferably, an isolated nucleicacid molecule of the invention that hybridizes under stringentconditions to the sequence of any of SEQ ID NOs: 1, 2, 31, 32, 51, 52,71, 72, 81, 82, 91, 92, 96, 97, 101, 102, 106, 107, 111, 112, 121, 122,141, 142, 151, 152, 161, 162, 171, 172, 181, 182, 191, 192, 201, 202,215, 217, 221, 222, 241, 242, 251, 252, 271, 272, 279, 280, 303, 304,308, 309, 324, 325, 329, 330, 351, 352, 362, 371, 372, 379, 380, 387,388, 403, 404, 415, 416, 423, 424, 437, 438, and the nucleotide sequenceof any of the clones deposited as ATCC® Accession numbers 207184,207219, 207220, 207221, 207228, 207230, PTA-147, PTA-150, PTA-151,PTA-295, PTA-424, PTA-438, PTA-455, PTA-817, PTA-1156, and PTA-1764, ora complement thereof, corresponds to a naturally-occurring nucleic acidmolecule. As used herein, a “naturally-occurring” nucleic acid moleculerefers to an RNA or DNA molecule having a nucleotide sequence thatoccurs in nature (e.g., encodes a natural protein).

[0892] In addition to naturally-occurring allelic variants of a nucleicacid molecule of the invention sequence that can exist in thepopulation, the skilled artisan will further appreciate that changes canbe introduced by mutation thereby leading to changes in the amino acidsequence of the encoded protein, without altering the biologicalactivity of the protein. For example, one can make nucleotidesubstitutions leading to amino acid substitutions at “non-essential”amino acid residues. A “non-essential” amino acid residue is a residuethat can be altered from the wild-type sequence without altering thebiological activity, whereas an “essential” amino acid residue isrequired for biological activity. For example, amino acid residues thatare not conserved or only semi-conserved among homologs of variousspecies may be non-essential for activity and thus would be likelytargets for alteration. Alternatively, amino acid residues that areconserved among the homologs of various species (e.g., murine and human)may be essential for activity and thus would not be likely targets foralteration.

[0893] Accordingly, another aspect of the invention pertains to nucleicacid molecules encoding a polypeptide of the invention that containchanges in amino acid residues that are not essential for activity. Suchpolypeptides differ in amino acid sequence from any of SEQ ID NOs: 3-8,33, 35, 38, 53-60, 73-78, 83-85, 93-95, 98-100, 103-105, 108-110,113-115, 123-131, 143-145, 153-160, 163, 173-175, 183-185, 193-198,203-214, 216, 223-236, 243-252, 253, 273-278, 281-302, 305-307, 310-315,326-328, 331-333, 353-358, 363-368, 373-378, 381-386, 389-394, 405-414,417-422, 425-436, and 439, yet retain biological activity. In oneembodiment, the isolated nucleic acid molecule includes a nucleotidesequence encoding a protein that includes an amino acid sequence that isat least about 40% identical, 50%, 60%, 70%, 80%, 90%, 95%, or 98%identical to the amino acid sequence of any of SEQ ID NOs: 3-8, 33, 35,38, 53-60, 73-78, 83-85, 93-95, 98-100, 103-105, 108-110, 113-115,123-131, 143-145, 153-160, 163, 173-175, 183-185, 193-198, 203-214, 216,223-236, 243-252, 253, 273-278, 281-302, 305-307, 310-315, 326-328,331-333, 353-358, 363-368, 373-378, 381-386, 389-394, 405-414, 417-422,425-436, and 439, or the amino acid sequence encoded by the nucleotidesequence of any of the clones deposited as ATCC® Accession numbers207184, 207219, 207220, 207221, 207228, 207230, PTA-147, PTA-150,PTA-151, PTA-295, PTA-424, PTA-438, PTA-455, PTA-817, PTA-1156, andPTA-1764.

[0894] An isolated nucleic acid molecule encoding a variant protein canbe created by introducing one or more nucleotide substitutions,additions or deletions into the nucleotide sequence of any of SEQ IDNOs: 1, 2, 31, 32, 51, 52, 71, 72, 81, 82, 91, 92, 96, 97, 101, 102,106, 107, 111, 112, 121, 122, 141, 142, 151, 152, 161, 162, 171, 172,181, 182, 191, 192, 201, 202, 215, 217, 221, 222, 241, 242, 251, 252,271, 272, 279, 280, 303, 304, 308, 309, 324, 325, 329, 330, 351, 352,362, 371, 372, 379, 380, 387, 388, 403, 404, 415, 416, 423, 424, 437,438, and the nucleotide sequence of any of the clones deposited as ATCC®Accession numbers 207184, 207219, 207220, 207221, 207228, 207230,PTA-147, PTA-150, PTA-151, PTA-295, PTA-424, PTA-438, PTA-455, PTA-817,PTA-1156, and PTA-1764, such that one or more amino acid residuesubstitutions, additions or deletions are introduced into the encodedprotein. Mutations can be introduced by standard techniques, such assite-directed mutagenesis and PCR-mediated mutagenesis. Preferably,conservative amino acid substitutions are made at one or more predictednon-essential amino acid residues. A “conservative amino acidsubstitution” is one in which the amino acid residue is replaced with anamino acid residue having a similar side chain. Families of amino acidresidues having similar side chains have been defined in the art. Thesefamilies include amino acids with basic side chains (e.g., lysine,arginine, histidine), acidic side chains (e.g., aspartic acid, glutamicacid), uncharged polar side chains (e.g., glycine, asparagine,glutamine, serine, threonine, tyrosine, cysteine), non-polar side chains(e.g., alanine, valine, leucine, isoleucine, proline, phenylalanine,methionine, tryptophan), beta-branched side chains (e.g., threonine,valine, isoleucine) and aromatic side chains (e.g., tyrosine,phenylalanine, tryptophan, histidine). Alternatively, mutations can beintroduced randomly along all or part of the coding sequence, such as bysaturation mutagenesis, and the resultant mutants can be screened forbiological activity to identify mutants that retain activity. Followingmutagenesis, the encoded protein can be expressed recombinantly and theactivity of the protein can be determined.

[0895] In one embodiment, a mutant polypeptide that is a variant of apolypeptide of the invention can be assayed for: (1) the ability to formprotein:protein interactions with a polypeptide of the invention; (2)the ability to bind a ligand of a polypeptide of the invention; (3) theability to bind with a modulator or substrate of a polypeptide of theinvention; (4) the ability to modulate a physiological activity of apolypeptide of the invention, such as one of those disclosed herein; or(5) the ability to catalyze a reaction catalyzed by a polypeptide of theinvention.

[0896] The present invention encompasses antisense nucleic acidmolecules, i.e., molecules which are complementary to a sense nucleicacid encoding a polypeptide of the invention, e.g., complementary to thecoding strand of a double-stranded cDNA molecule or complementary to anmRNA sequence. Accordingly, an antisense nucleic acid can hydrogen bondto a sense nucleic acid. The antisense nucleic acid can be complementaryto an entire coding strand, or to only a portion thereof, e.g., all orpart of the protein coding region (or open reading frame). An antisensenucleic acid molecule can be antisense to all or part of a non-codingregion of the coding strand of a nucleotide sequence encoding apolypeptide of the invention. The non-coding regions (“5′ and3′non-translated regions”) are the 5′ and 3′ sequences which flank thecoding region and are not translated into amino acids.

[0897] An antisense oligonucleotide can be, for example, about 5, 10,15, 20, 25, 30, 35, 40, 45, or 50 or more nucleotides in length. Anantisense nucleic acid of the invention can be constructed usingchemical synthesis and enzymatic ligation reactions using proceduresknown in the art. For example, an antisense nucleic acid (e.g., anantisense oligonucleotide) can be chemically synthesized using naturallyoccurring nucleotides or variously modified nucleotides designed toincrease the biological stability of the molecules or to increase thephysical stability of the duplex formed between the antisense and sensenucleic acids, e.g., phosphorothioate derivatives and acridinesubstituted nucleotides can be used. Examples of modified nucleotideswhich can be used to generate the antisense nucleic acid include5-fluorouracil, 5-bromouracil, 5-chlorouracil, 5-iodouracil,hypoxanthine, xanthine, 4-acetylcytosine, 5-(carboxyhydroxylmethyl)uracil, 5-carboxymethylaminomethyl-2-thiouridine,5-carboxymethylaminomethyluracil, dihydrouracil,beta-D-galactosylqueosine, inosine, N6-isopentenyladenine,1-methylguanine, 1-methylinosine, 2,2-dimethylguanine, 2-methyladenine,2-methylguanine, 3-methylcytosine, 5-methylcytosine, N6-adenine,7-methylguanine, 5-methylaminomethyluracil,5-methoxyaminomethyl-2-thiouracil, beta-D-mannosylqueosine,5′-methoxycarboxymethyluracil, 5-methoxyuracil,2-methylthio-N-6-isopentenyladenine, uracil-5-oxyacetic acid (v),wybutoxosine, pseudouracil, queosine, 2-thiocytosine,5-methyl-2-thiouracil, 2-thiouracil, 4-thiouracil, 5-methyluracil,uracil-5-oxyacetic acid methylester, uracil-5-oxyacetic acid (v),5-methyl-2-thiouracil, 3-(3-amino-3-N-2-carboxypropyl) uracil, (acp3)w,and 2,6-diaminopurine. Alternatively, the antisense nucleic acid can beproduced biologically using an expression vector into which a nucleicacid has been sub-cloned in an antisense orientation (i.e., RNAtranscribed from the inserted nucleic acid will be of an antisenseorientation to a target nucleic acid of interest, described further inthe following subsection).

[0898] The antisense nucleic acid molecules of the invention aretypically administered to a subject or generated in situ such that theyhybridize with or bind with cellular mRNA and/or genomic DNA encoding aselected polypeptide of the invention to thereby inhibit expression,e.g., by inhibiting transcription and/or translation. The hybridizationcan be by conventional nucleotide complementarity to form a stableduplex, or, for example, in the case of an antisense nucleic acidmolecule which binds with DNA duplexes, through specific interactions inthe major groove of the double helix. An example of a route ofadministration of antisense nucleic acid molecules of the inventionincludes direct injection at a tissue site. Alternatively, antisensenucleic acid molecules can be modified to target selected cells and thenadministered systemically. For example, for systemic administration,antisense molecules can be modified such that they specifically bindwith receptors or antigens expressed on a selected cell surface, e.g.,by linking the antisense nucleic acid molecules to peptides orantibodies which bind with cell surface receptors or antigens. Theantisense nucleic acid molecules can also be delivered to cells usingthe vectors described herein. To achieve sufficient intracellularconcentrations of the antisense molecules, vector constructs in whichthe antisense nucleic acid molecule is placed under the control of astrong pol II or pol III promoter are preferred.

[0899] An antisense nucleic acid molecule of the invention can be anα-anomeric nucleic acid molecule. An α-anomeric nucleic acid moleculeforms specific double-stranded hybrids with complementary RNA in whichthe strands run parallel to each other (Gaultier et al. (1987) NucleicAcids Res. 15:6625-6641). The antisense nucleic acid molecule can alsocomprise a 2′-o-methylribonucleotide (Inoue et al. (1987) Nucleic AcidsRes. 15:6131-6148) or a chimeric RNA-DNA analogue (Inoue et al. (1987)FEBS Lett. 215:327-330).

[0900] The invention also encompasses ribozymes. Ribozymes are catalyticRNA molecules which are capable of cleaving a single-stranded nucleicacid, such as an mRNA, to which they have a complementary region. Thus,ribozymes (e.g., hammerhead ribozymes as described in Haselhoff andGerlach (1988) Nature 334:585-591) can be used to catalytically cleavemRNA transcripts to thereby inhibit translation of the protein encodedby the mRNA. A ribozyme having specificity for a nucleic acid moleculeencoding a polypeptide of the invention can be designed based upon thenucleotide sequence of a cDNA disclosed herein. For example, aderivative of a Tetrahymena L-19 IVS RNA can be constructed in which thenucleotide sequence of the ribozyme active site is complementary to thenucleotide sequence to be cleaved, as described in Cech et al. U.S. Pat.No. 4,987,071; and Cech et al. U.S. Pat. No. 5,116,742. Alternatively,an mRNA encoding a polypeptide of the invention can be used to select acatalytic RNA having a specific ribonuclease activity from a pool of RNAmolecules. See, e.g., Bartel and Szostak (1993) Science 261:1411-1418.

[0901] The invention includes nucleic acid molecules which form triplehelical structures. For example, expression of a polypeptide of theinvention can be inhibited by targeting nucleotide sequencescomplementary to the regulatory region of the gene encoding thepolypeptide (e.g., the promoter and/or enhancer) to form triple helicalstructures that prevent transcription of the gene in target cells. Seegenerally Helene (1991) Anticancer Drug Des. 6(6):569-84; Helene (1992)Ann. N.Y. Acad. Sci. 660:27-36; and Maher (1992) Bioassays14(12):807-15. “Expression” of a polypeptide, as used herein, refersindividually and collectively to the processes of transcription of DNAto generate an RNA transcript and translation of an RNA to generate thepolypeptide.

[0902] In various embodiments, the nucleic acid molecules of theinvention can be modified at the base moiety, sugar moiety, or phosphatebackbone to improve, e.g., the stability, hybridization, or solubilityof the molecule. For example, the deoxyribose phosphate backbone of thenucleic acids can be modified to generate peptide nucleic acids (seeHyrup et al. (1996) Bioorganic & Medicinal Chemistry 4(1): 5-23). Asused herein, the terms “peptide nucleic acids” or “PNAs” refer tonucleic acid mimics, e.g., DNA mimics, in which the deoxyribosephosphate backbone is replaced by a pseudopeptide backbone and only thefour natural nucleobases are retained. The neutral backbone of PNAs hasbeen shown to allow specific hybridization with DNA and RNA underconditions of low ionic strength. Synthesis of PNA oligomers can beperformed using standard solid phase peptide synthesis protocols such asthose described in Hyrup et al. (1996), supra; Perry-O'Keefe et al.(1996) Proc. Natl. Acad. Sci. USA 93: 14670-675.

[0903] PNAs can be used in therapeutic and diagnostic applications. Forexample, PNAs can be used as antisense or anti-gene agents forsequence-specific modulation of gene expression by, e.g., inducingarrest of transcription or translation or by inhibiting replication.PNAs can also be used, e.g., in the analysis of single base pairmutations in a gene by, e.g., PNA directed PCR clamping; as artificialrestriction enzymes when used in combination with other enzymes, e.g.,S1 nucleases (Hyrup (1996), supra; or as probes or primers for DNAsequence and hybridization (Hyrup (1996), supra; Perry-O'Keefe et al.(1996) Proc. Natl. Acad. Sci. USA 93: 14670-675).

[0904] In another embodiment, PNAs can be modified, e.g., to enhancetheir stability or cellular uptake, by attaching lipophilic or otherhelper groups to PNA, by formation of PNA-DNA chimeras, or by use ofliposomes or other techniques of drug delivery known in the art. Forexample, PNA-DNA chimeras can be generated which can combine theadvantageous properties of PNA and DNA. Such chimeras allow DNArecognition enzymes, e.g., RNase H and DNA polymerases, to interact withthe DNA portion while the PNA portion providbs high binding affinity andspecificity. PNA-DNA chimeras can be linked using linkers of appropriatelengths selected in terms of base stacking, number of bonds between thenucleobases, and orientation (Hyrup (1996), supra). The synthesis ofPNA-DNA chimeras can be performed as described in Hyrup (1996), supra,and Finn et al. (1996) Nucleic Acids Res. 24(17):3357-63. For example, aDNA chain can be synthesized on a solid support using standardphosphoramidite coupling chemistry and modified nucleoside analogs.Compounds such as 5′-(4-methoxytrityl)amino-5′-deoxy-thymidinephosphoramidite can be used as a link between the PNA and the 5′ end ofDNA (Mag et al. (1989) Nucleic Acids Res. 17:5973-88). PNA monomers arethen coupled in a step-wise manner to produce a chimeric molecule with a5′ PNA segment and a 3′ DNA segment (Finn et al. (1996) Nucleic AcidsRes. 24(17):3357-63). Alternatively, chimeric molecules can besynthesized with a 5′ DNA segment and a 3′ PNA segment (Peterser et al.(1975) Bioorganic Med. Chem. Lett. 5:1119-11124).

[0905] In other embodiments, the oligonucleotide can include otherappended groups such as peptides (e.g., for targeting host cellreceptors in vivo), or agents facilitating transport across the cellmembrane (see, e.g., Letsinger et al. (1989) Proc. Natl. Acad. Sci. USA86:6553-6556; Lemaitre et al. (1987) Proc. Natl. Acad. Sci. USA84:648-652; PCT Publication No.

[0906] WO 88/09810) or the blood-brain barrier (see, e.g., PCTPublication No. WO 89/10134). In addition, oligonucleotides can bemodified with hybridization-triggered cleavage agents (see, e.g., Krolet al. (1988) Bio/Techniques 6:958-976) or intercalating agents (see,e.g., Zon (1988) Pharm. Res. 5:539-549). To this end, theoligonucleotide can be conjugated with another molecule, e.g., apeptide, hybridization triggered cross-linking agent, transport agent,hybridization-triggered cleavage agent, etc.

[0907] II. Isolated Proteins and Antibodies

[0908] One aspect of the invention pertains to isolated proteins, andbiologically active portions thereof, as well as polypeptide fragmentssuitable for use as immunogens to generate antibodies directed against apolypeptide of the invention. In one embodiment, the native polypeptideis isolated from cells or tissue sources by an appropriate purificationscheme using standard protein purification techniques. In anotherembodiment, polypeptides of the invention are produced by recombinantDNA techniques. As an alternative to recombinant expression, apolypeptide of the invention can be synthesized chemically usingstandard peptide synthesis techniques.

[0909] An “isolated” or “purified” protein or biologically activeportion thereof is substantially free of cellular material or othercontaminating proteins from the cell or tissue source from which theprotein is derived, or substantially free of chemical precursors orother chemicals, when chemically synthesized. The language“substantially free of cellular material” includes preparations ofprotein in which the protein is separated from cellular components ofthe cells from which it is isolated or recombinantly produced. Thus,protein that is substantially free of cellular material includespreparations of protein having less than about 30%, 20%, 10%, or 5% (bydry weight) of heterologous protein (also referred to herein as a“contaminating protein”). When the protein or biologically activeportion thereof is recombinantly produced, it is also preferablysubstantially free of culture medium, i.e., culture medium representsless than about 20%, 10%, or 5% of the volume of the proteinpreparation. When the protein is produced by chemical synthesis, it ispreferably substantially free of chemical precursors or other chemicals,i.e., it is separated from chemical precursors or other chemicals whichare involved in the synthesis of the protein. Accordingly suchpreparations of the protein have less than about 30%, 20%, 10%, 5% (bydry weight) of chemical precursors or compounds other than thepolypeptide of interest.

[0910] Biologically active portions of a polypeptide of the inventioninclude polypeptide regions having an amino acid sequence sufficientlyidentical to or derived from the amino acid sequence of the protein(e.g., the amino acid sequence shown in any of SEQ ID NOs: 3-8, 33, 35,38, 53-60, 73-78, 83-85, 93-95, 98-100, 103-105, 108-110, 113-115,123-131, 143-145, 153-160, 163, 173-175, 183-185, 193-198, 203-214, 216,223-236, 243-252, 253, 273-278, 281-302, 305-307, 310-315, 326-328,331-333, 353-358, 363-368, 373-378, 381-386, 389-394, 405-414, 417-422,425-436, and 439, or the amino acid sequence encoded by the nucleotidesequence of any of the clones deposited as ATCC® Accession numbers207184, 207219, 207220, 207221, 207228, 207230, PTA-147, PTA-150,PTA-151, PTA-295, PTA-424, PTA-438, PTA-455, PTA-817, PTA-1156, andPTA-1764), which include fewer amino acids than the full length protein,and exhibit at least one activity of the corresponding full-lengthprotein. Typically, biologically active portions comprise a domain ormotif with at least one activity of the corresponding protein. Abiologically active portion of a protein of the invention can be apolypeptide which is, for example, 10, 25, 50, 100 or more amino acidsin length. Moreover, other biologically active portions, in which otherregions of the protein are deleted, can be prepared by recombinanttechniques and evaluated for one or more of the functional activities ofthe native form of a polypeptide of the invention.

[0911] Examples of polypeptides have the amino acid sequence of any ofSEQ ID NOs: 3-8, 33, 35, 38, 53-60, 73-78, 83-85, 93-95, 98-100,103-105, 108-110, 113-115, 123-131, 143-145, 153-160, 163, 173-175,183-185, 193-198, 203-214, 216, 223-236, 243-252, 253, 273-278, 281-302,305-307, 310-315, 326-328, 331-333, 353-358, 363-368, 373-378, 381-386,389-394, 405-414, 417-422, 425-436, and 439 or the amino acid sequenceencoded by the nucleotide sequence of any of the clones deposited asATCC® Accession numbers 207184, 207219, 207220, 207221, 207228, 207230,PTA-147, PTA-150, PTA-151, PTA-295, PTA-424, PTA-438, PTA-455, PTA-817,PTA-1156, and PTA-1764. Other useful proteins are substantiallyidentical (e.g., at least about 40%, preferably 50%, 60%, 70%, 80%, 90%,95%, or 99%) to any of SEQ ID NOs: 3-8, 33, 35, 38, 53-60, 73-78, 83-85,93-95, 98-100, 103-105, 108-110, 113-115, 123-131, 143-145,153-160,163,173-175, 183-185, 193-198,203-214, 216, 223-236, 243-252,253, 273-278, 281-302, 305-307, 310-315, 326-328, 331-333, 353-358,363-368, 373-378, 381-386, 389-394, 405-414, 417-422, 425-436, and 439or the amino acid sequence encoded by the nucleotide sequence of any ofthe clones deposited as ATCC® Accession numbers 207184, 207219, 207220,207221, 207228, 207230, PTA-147, PTA-150, PTA-151, PTA-295, PTA-424,PTA-438, PTA-455, PTA-817, PTA-1156, and PTA-1764 and retain thefunctional activity of the protein of the correspondingnaturally-occurring protein. Such proteins can differ in amino acidsequence owing, for example, to natural allelic variation ormutagenesis.

[0912] The invention also provides chimeric or fusion proteins. As usedherein, a “chimeric protein” or “fusion protein” comprises all or part(preferably biologically active) of a polypeptide of the inventionoperably linked with a heterologous polypeptide (i.e., a polypeptideother than the same polypeptide of the invention). Within the fusionprotein, the term “operably linked” is intended to indicate that thepolypeptide of the invention and the heterologous polypeptide are fusedin-frame with each other. The heterologous polypeptide can be fused withthe amino-terminus or the carboxyl-terminus of the polypeptide of theinvention.

[0913] One useful fusion protein is a GST fusion protein in which thepolypeptide of the invention is fused with the carboxyl terminus of GSTsequences. Such fusion proteins can facilitate purification of arecombinant polypeptide of the invention.

[0914] In another embodiment, the fusion protein contains a heterologoussignal sequence at its amino terminus. For example, the native signalsequence of a polypeptide of the invention can be removed and replacedwith a signal sequence from another protein. For example, the gp67secretory sequence of the baculovirus envelope protein can be used as aheterologous signal sequence (Current Protocols in Molecular Biology,Ausubel et al., eds., John Wiley & Sons, 1992). Other examples ofeukaryotic heterologous signal sequences include the secretory sequencesof melittin and human placental alkaline phosphatase (Stratagene; LaJolla, Calif.). In yet another example, useful prokaryotic heterologoussignal sequences include the phoA secretory signal (Sambrook et al.,supra) and the protein A secretory signal (Pharmacia Biotech;Piscataway, N.J.).

[0915] In yet another embodiment, the fusion protein is animmunoglobulin fusion protein in which all or part of a polypeptide ofthe invention is fused with sequences derived from a member of theimmunoglobulin protein family. The immunoglobulin fusion proteins of theinvention can be incorporated into pharmaceutical compositions andadministered to a subject to inhibit an interaction between a ligand(soluble or membrane-bound) and a protein on the surface of a cell(receptor), to thereby suppress signal transduction in vivo. Theimmunoglobulin fusion protein can be used to affect the bioavailabilityof a cognate ligand of a polypeptide of the invention. Inhibition ofligand/receptor interaction can be useful therapeutically, both fortreating proliferative and differentiative disorders and for modulating(e.g., promoting or inhibiting) cell survival. Moreover, theimrmunoglobulin fusion proteins of the invention can be used asimmunogens to produce antibodies directed against a polypeptide of theinvention in a subject, to purify ligands and in screening assays toidentify molecules which inhibit the interaction of receptors withligands. The immunoglobulin fusion protein can, for example, comprise aportion of a polypeptide of the invention fused with the amino-terminusor the carboxyl-terminus of an immunoglobulin constant region, asdisclosed in U.S. Pat. No. 5,714,147, U.S. Pat. No. 5,116,964, U.S. Pat.No. 5,514,582, and U.S. Pat. No. 5,455,165.

[0916] Chimeric and fusion proteins of the invention can be produced bystandard recombinant DNA techniques. In another embodiment, the fusiongene can be synthesized by conventional techniques including automatedDNA synthesizers. Alternatively, PCR amplification of gene fragments canbe performed using anchor primers which give rise to complementaryoverhangs between two consecutive gene fragments and which cansubsequently be annealed and re-amplified to generate a chimeric genesequence (see, e.g., Ausubel et al., supra). Moreover, many expressionvectors are commercially available that already encode a fusion moiety(e.g., a GST polypeptide). A nucleic acid encoding a polypeptide of theinvention can be cloned into such an expression vector such that thefusion moiety is linked in-frame to the polypeptide of the invention.

[0917] A signal sequence of a polypeptide of the invention (e.g., thesignal sequence in any of SEQ ID NOs: 3, 33, 53, 73, 83, 93, 98, 103,108, 113, 123, 143, 153, 163, 173, 183, 193, 203, 216, 223, 243, 253,273, 281, 305, 310, 326, 331, 353, 363, 381, 389, 405, 417, 425, and439) can be used to facilitate secretion and isolation of the secretedprotein or another protein of interest. Signal sequences are typicallycharacterized by a core of hydrophobic amino acids which are generallycleaved from the mature protein during secretion in one or more cleavageevents. Such signal peptides contain processing sites that allowcleavage of the signal sequence from the mature proteins as they passthrough the secretory pathway. Thus, the invention pertains to thedescribed polypeptides having a signal sequence, as well as to thesignal sequence itself and to the polypeptide in the absence of thesignal sequence (i.e., the cleavage products). In one embodiment, anucleic acid sequence encoding a signal sequence of the invention can beoperably linked in an expression vector with a protein of interest, suchas a protein which is ordinarily not secreted or is otherwise difficultto isolate. The signal sequence directs secretion of the protein, suchas from a eukaryotic host into which the expression vector istransformed, and the signal sequence is subsequently or concurrentlycleaved. The protein can then be readily purified from the extracellularmedium by art recognized methods. Alternatively, the signal sequence canbe linked with the protein of interest using a sequence whichfacilitates purification, such as with a GST domain.

[0918] In another embodiment, the signal sequences of the presentinvention can be used to identify regulatory sequences, e.g., promoters,enhancers, repressors. Since signal sequences are the mostamino-terminal sequences of a peptide, the nucleic acids which flank thesignal sequence on its amino-terminal side are likely regulatorysequences which affect transcription. Thus, a nucleotide sequence whichencodes all or a portion of a signal sequence can be used as a probe toidentify and isolate signal sequences and their flanking regions, andthese flanking regions can be studied to identify regulatory elementstherein.

[0919] The present invention also pertains to variants of thepolypeptides of the invention. Such variants have an altered amino acidsequence which can function as either agonists (mimetics) or asantagonists. Variants can be generated by mutagenesis, e.g., discretepoint mutation or truncation. An agonist can retain substantially thesame, or a subset, of the biological activities of the naturallyoccurring form of the protein. An antagonist of a protein can inhibitone or more of the activities of the naturally occurring form of theprotein by, for example, competitively binding with a downstream orupstream member of a cellular signaling cascade which includes theprotein of interest. Thus, specific biological effects can be elicitedby treatment with a variant of limited function. Treatment of a subjectwith a variant having a subset of the biological activities of thenaturally occurring form of the protein can have fewer side effects in asubject, relative to treatment with the naturally occurring form of theprotein.

[0920] Variants of a protein of the invention which function as eitheragonists (e.g., mimetics) or as antagonists can be identified byscreening combinatorial libraries of mutants, e.g., truncation mutants,of the protein of the invention for agonist or antagonist activity. Inone embodiment, a variegated library of variants is generated bycombinatorial mutagenesis at the nucleic acid level and is encoded by avariegated gene library. A variegated library of variants can beproduced by, for example, enzymatically ligating a mixture of syntheticoligonucleotides into gene sequences such that a degenerate set ofpotential protein sequences can be expressed as individual polypeptides,or alternatively, as a set of larger fusion proteins (e.g., for phagedisplay). There are a variety of methods which can be used to producelibraries of potential variants of the polypeptides of the inventionfrom a degenerate oligonucleotide sequence. Methods for synthesizingdegenerate oligonucleotides are known in the art (see, e.g., Narang(1983) Tetrahedron 39:3; Itakura et al. (1984) Annu. Rev.

[0921] Biochem. 53:323; Itakura et al. (1984) Science 198:1056; Ike etal. (1983) Nucleic Acid Res. 11:477).

[0922] In addition, libraries of fragments of the coding sequence of apolypeptide of the invention can be used to generate a variegatedpopulation of polypeptides for screening and subsequent selection ofvariants. For example, a library of coding sequence fragments can begenerated by treating a double stranded PCR fragment of the codingsequence of interest with a nuclease under conditions wherein nickingoccurs only about once per molecule, denaturing the double stranded DNA,re-naturing the DNA to form double stranded DNA which can includesense/antisense pairs from different nicked products, removing singlestranded portions from reformed duplexes by treatment with S1 nuclease,and ligating the resulting fragment library into an expression vector.By this method, an expression library can be derived which encodes aminoterminal and internal fragments of various sizes of the protein ofinterest.

[0923] Several techniques are known in the art for screening geneproducts of combinatorial libraries made by point mutations ortruncation, and for screening cDNA libraries for gene products having aselected property. The most widely used techniques, which are amenableto high through-put analysis, for screening large gene librariestypically include cloning the gene library into replicable expressionvectors, transforming appropriate cells with the resulting library ofvectors, and expressing the combinatorial genes under conditions inwhich detection of a desired activity facilitates isolation of thevector encoding the gene whose product was detected. Recursive ensemblemutagenesis (REM), a technique which enhances the frequency offunctional mutants in the libraries, can be used in combination with thescreening assays to identify variants of a protein of the invention(Arkin and Yourvan (1992) Proc. Natl. Acad. Sci. USA 89:7811-7815;Delgrave et al. (1993) Protein Engineering 6(3):327-331).

[0924] An isolated polypeptide of the invention, or a fragment thereof,can be used as an immunogen to generate antibodies using standardtechniques for polyclonal and monoclonal antibody preparation. Thefull-length polypeptide or protein can be used or, alternatively, theinvention provides antigenic peptide fragments for use as immunogens.The antigenic peptide of a protein of the invention comprises at least10 (preferably 12, 15, 20, or 30 or more) amino acid residues of theamino acid sequence of any of SEQ ID NOs: 3-8, 33, 35, 38, 53-60, 73-78,83-85, 93-95, 98-100, 103-105, 108-110, 113-115, 123-131, 143-145,153-160, 163, 173-175, 183-185, 193-198, 203-214, 216, 223-236, 243-252,253, 273-278-, 281-302, 305-307, 310-315, 326-328, 331-333, 353-358,363-368, 373-378, 381-386, 389-394, 405-414, 417-422, 425-436, and 439or the amino acid sequence encoded by the nucleotide sequence of any ofthe clones deposited as ATCC® Accession numbers 207184, 207219, 207220,207221, 207228, 207230, PTA-147, PTA-150, PTA-151, PTA-295, PTA-424,PTA-438, PTA-455, PTA-817, PTA-1156, and PTA-1764, and encompasses anepitope of the protein such that an antibody raised against the peptideforms a specific immune complex with the protein.

[0925] Examples of epitopes encompassed by the antigenic peptide areregions that are located on the surface of the protein, e.g.,hydrophilic regions. FIGS. 3, 8, 10G, 11Y-1 through 11Y-6, 11Z-6, 12D,13B, 14B, 15E, 15J, 16E, 17G, 18D, 18G, 19F, 19L, 20D, 21E, 22D, 22M,23D, 24F, 25L, 25M, 26J, 27U, 28E, 29F, and 30D are hydrophobicity plotsof proteins of the invention. These or similar analyses can be used toidentify hydrophilic regions.

[0926] An immunogen typically is used to prepare antibodies byimmunizing a suitable (i.e., immunocompetent) subject such as a rabbit,goat, mouse, or other mammal or vertebrate. An appropriate immunogenicpreparation-can contain, for example, recombinantly-expressed orchemically-synthesized polypeptide. The preparation can further includean adjuvant, such as Freund's complete or incomplete adjuvant, or asimilar immunostimulatory agent.

[0927] Accordingly, another aspect of the invention pertains toantibodies directed against a polypeptide of the invention. The terms“antibody” and “antibody substance” as used interchangeably herein referto immunoglobulin molecules and immunologically active portions ofimmunoglobulin molecules, i.e., molecules that contain an antigenbinding site which specifically binds an antigen, such as a polypeptideof the invention. A molecule which specifically binds with a givenpolypeptide of the invention is a molecule which binds the polypeptide,but does not substantially bind other molecules in a sample, e.g., abiological sample, which naturally contains the polypeptide. Examples ofimmunologically active portions of immunoglobulin molecules includeF(ab) and F(ab′)₂ fragments which can be generated by treating theantibody with an enzyme such as pepsin. The invention providespolyclonal and monoclonal antibodies. The term “monoclonal antibody” or“monoclonal antibody composition”, as used herein, refers to apopulation of antibody molecules that contain only one species of anantigen binding site capable of immunoreacting with a particularepitope.

[0928] Polyclonal antibodies can be prepared as described above byimmunizing a suitable subject with a polypeptide of the invention as animmunogen. The antibody titer in the immunized subject can be monitoredover time by standard techniques, such as with an enzyme linkedimmunosorbent assay (ELISA) using immobilized polypeptide. If desired,the antibody molecules can be harvested or isolated from the subject(e.g., from the blood or serum of the subject) and further purified bywell-known techniques, such as protein A chromatography to obtain theIgG fraction. At an appropriate time after immunization, e.g., when thespecific antibody titers are highest, antibody-producing cells can beobtained from the subject and used to prepare monoclonal antibodies bystandard techniques, such as the hybridoma technique originallydescribed by Kohler and Milstein (1975) Nature 256:495-497, the human Bcell hybridoma technique (Kozbor et al. (1983) Immunol. Today 4:72), theEBV-hybridoma technique (Cole et al. (1985), Monoclonal Antibodies andCancer Therapy, Alan R. Liss, Inc., pp. 77-96) or trioma techniques. Thetechnology for producing hybridomas is well known (see generally CurrentProtocols in Immunology (1994) Coligan et al. (Eds.) John Wiley & Sons,Inc., New York, N.Y.). Hybridoma cells producing a monoclonal antibodyof the invention are detected by screening the hybridoma culturesupernatants for antibodies that bind the polypeptide of interest, e.g.,using a standard ELISA assay.

[0929] Alternative to preparing monoclonal antibody-secretinghybridomas, a monoclonal antibody directed against a polypeptide of theinvention can be identified and isolated by screening a recombinantcombinatorial immunoglobulin library (e.g., an antibody phage displaylibrary) with the polypeptide of interest. Kits for generating andscreening phage display libraries are commercially available (e.g., thePharmacia Recombinant Phage Antibody System, Catalog No. 27-9400-01; andthe Stratagene SurfZAP Phage Display Kit, Catalog No. 240612).Additionally, examples of methods and reagents particularly amenable foruse in generating and screening antibody display library can be foundin, for example, U.S. Pat. No. 5,223,409; PCT Publication No. WO92/18619; PCT Publication No. WO 91/17271; PCT Publication No. WO92/20791; PCT Publication No. WO 92/15679; PCT Publication No. WO93/01288; PCT Publication No. WO 92/01047; PCT Publication No. WO92/09690; PCT Publication No. WO 90/02809; Fuchs et al. (1991)Bio/Technology 9:1370-1372; Hay et al. (1992) Hum. Antibod. Hybridomas3:81-85; Huse et al. (1989) Science 246:1275-1281; Griffiths et al.(1993) EMBO J. 12:725-734.

[0930] Recombinant antibodies, such as chimeric and humanized monoclonalantibodies, comprising both human and non-human portions, which can bemade using standard recombinant DNA techniques, are within the scope ofthe invention. Such chimeric and humanized monoclonal antibodies can beproduced by recombinant DNA techniques known in the art, for exampleusing methods described in PCT Publication No. WO 87/02671; EuropeanPatent Application 184,187; European Patent Application 171,496;European Patent Application 173,494; PCT Publication No. WO 86/01533;U.S. Pat. No. 4,816,567; European Patent Application 125,023; Better etal. (1988) Science 240:1041-1043; Liu et al. (1987) Proc. Natl. Acad.Sci. USA 84:3439-3443; Liu et al. (1987) J. Immunol. 139:3521-3526; Sunet al. (1987) Proc. Natl. Acad. Sci. USA 84:214-218; Nishimura et al.(1987) Cancer Res. 47:999-1005; Wood et al. (1985) Nature 314:446-449;and Shaw et al. (1988) J. Natl. Cancer Inst. 80:1553-1559); Morrison(1985) Science 229:1202-1207; Oi et al. (1986) Bio/Techniques 4:214;U.S. Pat. No. 5,225,539; Jones et al. (1986) Nature 321:552-525;Verhoeyan et al. (1988) Science 239:1534; and Beidler et al. (1988) J.Immunol. 141:4053-4060.

[0931] Completely human antibodies are particularly desirable fortherapeutic treatment of human patients. Such antibodies can be producedusing transgenic mice which are incapable of expressing endogenousimmunoglobulin heavy and light chains genes, but which can express humanheavy and light chain genes. The transgenic mice are immunized in thenormal fashion with a selected antigen, e.g., all or a portion of apolypeptide of the invention. Monoclonal antibodies directed against theantigen can be obtained using conventional hybridoma technology. Thehuman immunoglobulin transgenes harbored by the transgenic micerearrange during B cell differentiation, and subsequently undergo classswitching and somatic mutation. Thus, using such a technique, it ispossible to produce therapeutically useful IgG, IgA, and IgE antibodies.For an overview of this technology for producing human antibodies, seeLonberg and Huszar (1995, Int. Rev. Immunol. 13:65-93). For a detaileddiscussion of this technology for producing human antibodies and humanmonoclonal antibodies and protocols for producing such antibodies, see,e.g., U.S. Pat. No. 5,625,126; U.S. Pat. No. 5,633,425; U.S. Pat. No.5,569,825; U.S. Pat. No. 5,661,016; and U.S. Pat. No. 5,545,806. Inaddition, companies such as Abgenix, Inc. (Freemont, Calif.), can beengaged to provide human antibodies directed against a selected antigenusing technology similar to that described above.

[0932] Completely human antibodies which recognize a selected epitopecan be generated using a technique referred to as “guided selection.” Inthis approach a selected non-human monoclonal antibody, e.g., a murineantibody, is used to guide the selection of a completely human antibodyrecognizing the same epitope (Jespers et al. (1994) Bio/technology12:899-903).

[0933] An antibody directed against a polypeptide of the invention(e.g., monoclonal antibody) can be used to isolate the polypeptide bystandard techniques, such as affinity chromatography orimmunoprecipitation. Moreover, such an antibody can be used to detectthe protein (e.g., in a cellular lysate or cell supernatant) in order toevaluate the abundance and pattern of expression of the polypeptide. Theantibodies can also be used diagnostically to monitor protein levels intissue as part of a clinical testing procedure, e.g., to, for example,determine the efficacy of a given treatment regimen. Detection can befacilitated by coupling the antibody to a detectable substance. Examplesof detectable substances include various enzymes, prosthetic groups,fluorescent materials, luminescent materials, bioluminescent materials,and radioactive materials. Examples of suitable enzymes includehorseradish peroxidase, alkaline phosphatase, β-galactosidase, oracetylcholinesterase; examples of suitable prosthetic group complexesinclude streptavidin/biotin and avidin/biotin; examples of suitablefluorescent materials include umbelliferone, fluorescein, fluoresceinisothiocyanate, rhodamine, dichlorotriazinylamine fluorescein, dansylchloride or phycoerythrin; an example of a luminescent material includesluminol; examples of bioluminescent materials include luciferase,luciferin, and aequorin, and examples of suitable radioactive materialinclude ¹²⁵I, ¹³¹I, ³⁵S or ³H.

[0934] An antibody (or fragment thereof) can be conjugated to atherapeutic moiety such as a cytotoxin, a therapeutic agent, or aradioactive agent (e.g., a radioactive metal ion). Cytotoxins andcytotoxic agents include any agent that is detrimental to cells.Examples of such agents include taxol, cytochalasin B, gramicidin D,ethidium bromide, emetine, mitomycin, etoposide, tenoposide,vincristine, vinblastine, colchicin, doxorubicin, daunorubicin,dihydroxy anthracin dione, mitoxantrone, mithramycin, actinomycin D,1-dehydrotestosterone, glucocorticoids, procaine, tetracaine, lidocaine,propranolol, and puromycin and analogs or homologs thereof. Therapeuticagents include, but are not limited to, antimetabolites (e.g.,methotrexate, 6-mercaptopurine, 6-thioguanine, cytarabine, and5-fluorouracil decarbazine), alkylating agents (e.g., mechlorethamine,thioepa chlorambucil, melphalan, carmustine (BSNU) and lomustine (CCNU),cyclothosphamide, busulfan, dibromomannitol, streptozotocin, mitomycinC, and cis-dichlorodiamine platinum (II) (DDP) cisplatin),anthracyclines (e.g., daunorubicin {formerly designated daunomycin} anddoxorubicin), antibiotics (e.g., dactinomycin {formerly designatedactinomycin}, bleomycin, mithramycin, and anthramycin), and anti-mitoticagents (e.g., vincristine and vinblastine).

[0935] Conjugated antibodies of the invention can be used for modifyinga given biological response, the drug moiety not being limited toclassical chemical therapeutic agents. For example, the drug moiety canbe a protein or polypeptide possessing a desired biological activity.Such proteins include, for example, toxins such as abrin, ricin A,Pseudomonas exotoxin, or diphtheria toxin; proteins such as tumornecrosis factor, alpha-interferon, beta-interferon, nerve growth factor,platelet derived growth factor, tissue plasminogen activator; andbiological response modifiers such as lymphokines, interleukin-1,interleukin-2, interleukin-6, granulocyte macrophage colony stimulatingfactor, granulocyte colony stimulating factor, or other growth factors.

[0936] Techniques for conjugating a therapeutic moiety to an antibodyare well known (see, e.g., Arnon et al., 1985, “Monoclonal AntibodiesFor Immunotargeting Of Drugs In Cancer Therapy”, in MonoclonalAntibodies And Cancer Therapy, Reisfeld et al., Eds., Alan R. Liss, Inc.pp. 243-256; Hellstrom et al., 1987, “Antibodies For Drug Delivery”, inControlled Drug Delivery, 2nd ed., Robinson et al., Eds., Marcel Dekker,Inc., pp. 623-653; Thorpe, 1985, “Antibody Carriers Of Cytotoxic AgentsIn Cancer Therapy: A Review”, in Monoclonal Antibodies '84: BiologicalAnd Clinical Applications, Pinchera et al., Eds., pp. 475-506;“Analysis, Results, And Future Prospective Of The Therapeutic Use OfRadiolabeled Antibody In Cancer Therapy”, in Monoclonal Antibodies ForCancer Detection And Therapy, Baldwin et al., Eds., Academic Press, pp.303-316, 1985; and Thorpe et al., 1982, Immunol. Rev., 62:119-158).Alternatively, an antibody can be conjugated to a second antibody toform an antibody heteroconjugate as described by Segal in U.S. Pat. No.4,676,980.

[0937] III. Recombinant Expression Vectors and Host Cells

[0938] Another aspect of the invention pertains to vectors, includingexpression vectors, containing a nucleic acid encoding a polypeptide ofthe invention (or a portion thereof). As used herein, the term “vector”refers to a nucleic acid molecule capable of transporting anothernucleic acid to which it has been linked. One type of vector is a“plasmid”, which refers to a circular double stranded DNA loop intowhich additional DNA segments can be ligated. Another type of vector isa viral vector, wherein additional DNA segments can be ligated into theviral genome. Certain vectors are capable of autonomous replication in ahost cell into which they are introduced (e.g., bacterial vectors havinga bacterial origin of replication and episomal mammalian vectors). Othervectors (e.g., non-episomal mammalian vectors) are integrated into thegenome of a host cell upon introduction into the host cell, and therebyare replicated along with the host genome. Moreover, certain vectors,designated expression vectors, are capable of directing expression ofgenes with which they are operably linked. In general, expressionvectors of utility in recombinant DNA techniques are often in the formof plasmids (vectors). However, the invention is intended to includesuch other forms of expression vectors, such as viral vectors (e.g.,replication defective retroviruses, adenoviruses and adeno-associatedviruses), which serve equivalent functions.

[0939] The recombinant expression vectors of the invention comprise anucleic acid of the invention in a form suitable for expression of thenucleic acid in a host cell. This means that the recombinant expressionvectors include one or more regulatory sequences, selected on the basisof the host cells to be used for expression, which is operably linkedwith the nucleic acid sequence to be expressed. Within a recombinantexpression vector, “operably linked” is intended to mean that thenucleotide sequence of interest is linked with the regulatorysequence(s) in a manner which allows expression of the nucleotidesequence (e.g., in an in vitro transcription/translation system or in ahost cell when the vector is introduced into the host cell). The term“regulatory sequence” is intended to include promoters, enhancers andother expression control elements (e.g., polyadenylation signals). Suchregulatory sequences are described, for example, in Goeddel, GeneExpression Technology: Methods in Enzymology 185, Academic Press, SanDiego, Calif. (1990). Regulatory sequences include those which directconstitutive expression of a nucleotide sequence in many types of hostcell and those which direct expression of the nucleotide sequence onlyin certain host cells (e.g., tissue-specific regulatory sequences). Itwill be appreciated by those skilled in the art that the design of theexpression vector can depend on such factors as the choice of the hostcell to be transformed, and the level of expression of protein desired.The expression vectors of the invention can be introduced into hostcells to thereby produce proteins or peptides, including fusion proteinsor peptides, encoded by nucleic acids as described herein.

[0940] The recombinant expression vectors of the invention can bedesigned for expression of a polypeptide of the invention in prokaryotic(e.g., E. coli) or eukaryotic cells (e.g., insect cells (usingbaculovirus expression vectors), yeast cells or mammalian cells).Suitable host cells are discussed further in Goeddel, supra.Alternatively, the recombinant expression vector can be transcribed andtranslated in vitro, for example using T7 promoter regulatory sequencesand T7 polymerase.

[0941] Expression of proteins in prokaryotes is most often carried outin E. coli with vectors containing constitutive or inducible promotersdirecting the expression of either fusion or non-fusion proteins. Fusionvectors add a number of amino acids to a protein encoded therein,usually to the amino terminus of the recombinant protein. Such fusionvectors typically serve three purposes: 1) to increase expression ofrecombinant protein; 2) to increase the solubility of the recombinantprotein; and 3) to aid in the purification of the recombinant protein byacting as a ligand in affinity purification. Often, in fusion expressionvectors, a proteolytic cleavage site is introduced at the junction ofthe fusion moiety and the recombinant protein to enable separation ofthe recombinant protein from the fusion moiety subsequent topurification of the fusion protein. Such enzymes, and their cognaterecognition sequences, include Factor Xa, thrombin and enterokinase.Typical fusion expression vectors include pGEX (Pharmacia Biotech Inc;Smith and Johnson (1988) Gene 67:31-40), pMAL (New England Biolabs,Beverly, Mass.) and pRIT5 (Pharmacia, Piscataway, N.J.) which fuseglutathione S-transferase (GST), maltose E binding protein, or proteinA, respectively, to the target recombinant protein.

[0942] Examples of suitable inducible non-fusion E. coli expressionvectors include pTrc (Amann et al., (1988) Gene 69:301-315) and pET 11d(Studier et al., Gene Expression Technology: Methods in Enzymology 185,Academic Press, San Diego, Calif. (1990) 60-89). Target gene expressionfrom the pTrc vector relies on host RNA polymerase transcription from ahybrid trp-lac fusion promoter. Target gene expression from the pET 11dvector relies on transcription from a T7 gn10-lac fusion promotermediated by a co-expressed viral RNA polymerase (T7 gn1). This viralpolymerase is supplied by host strains BL21(DE3) or HMS174(DE3) from aresident λ prophage harboring a T7 gn1 gene under the transcriptionalcontrol of the lacUV 5 promoter.

[0943] One strategy to maximize recombinant protein expression in E.coli is to express the protein in a host bacteria having an impairedcapacity to proteolytically cleave the recombinant protein (Gottesman,Gene Expression Technology: Methods in Enzymology 185, Academic Press,San Diego, Calif. (1990) 119-128). Another strategy is to alter thenucleic acid sequence of the nucleic acid to be inserted into anexpression vector such that the individual codons for each amino acidare those preferentially used in E. coli (Wada et al. (1992) NucleicAcids Res. 20:2111-2118). Such alteration of nucleic acid sequences ofthe invention can be performed by standard DNA synthesis techniques.

[0944] In another embodiment, the expression vector is a yeastexpression vector. Examples of vectors for expression in yeast S.cerevisiae include pYepSec1 (Baldari et al. (1987) EMBO J. 6:229-234),pMFa (Kurjan and Herskowitz, (1982) Cell 30:933-943), pJRY88 (Schultz etal. (1987) Gene 54:113-123), pYES2 (Invitrogen Corporation, San Diego,Calif.), and pPicZ (Invitrogen Corp, San Diego, Calif.).

[0945] Alternatively, the expression vector is a baculovirus expressionvector. Baculovirus vectors available for expression of proteins incultured insect cells (e.g., Sf 9 cells) include the pAc series (Smithet al. (1983) Mol. Cell Biol. 3:2156-2165) and the pVL series (Lucklowand Summers (1989) Virology 170:31-39).

[0946] In yet another embodiment, a nucleic acid of the invention isexpressed in mammalian cells using a mammalian expression vector.Examples of mammalian expression vectors include pCDM8 (Seed (1987)Nature 329:840) and pMT2PC (Kaufman et al. (1987) EMBO J. 6:187-195).When used in mammalian cells, the expression vector's control functionsare often provided by viral regulatory elements. For example, commonlyused promoters are derived from polyoma, Adenovirus 2, cytomegalovirusand Simian Virus 40. For other suitable expression systems for bothprokaryotic and eukaryotic cells see chapters 16 and 17 of Sambrook etal., supra.

[0947] In another embodiment, the recombinant mammalian expressionvector is capable of directing expression of the nucleic acidpreferentially in a particular cell type (e.g., tissue-specificregulatory elements are used to express the nucleic acid).Tissue-specific regulatory elements are known in the art. Non-limitingexamples of suitable tissue-specific promoters include the albuminpromoter (liver-specific; Pinkert et al. (1987) Genes Dev. 1:268-277),lymphoid-specific promoters (Calame and Eaton (1988) Adv. Immunol.43:235-275), in particular promoters of T cell receptors (Winoto andBaltimore (1989) EMBO J. 8:729-733) and immunoglobulins (Banerji et al.(1983) Cell 33:729-740; Queen and Baltimore (1983) Cell 33:741-748),neuron-specific promoters (e.g., the neurofilament promoter; Byrne andRuddle (1989) Proc. Natl. Acad. Sci. USA 86:5473-5477),pancreas-specific promoters (Edlund et al. (1985) Science 230:912-916),and mammary gland-specific promoters (e.g., milk whey promoter; U.S.Pat. No. 4,873,316 and European Application Publication No. 264,166).Developmentally-regulated promoters are also encompassed, for examplethe murine hox promoters (Kessel and Gruss (1990) Science 249:374-379)and the α-fetoprotein promoter (Campes and Tilghman (1989) Genes Dev.3:537-546).

[0948] The invention further provides a recombinant expression vectorcomprising a DNA molecule of the invention cloned into the expressionvector in an antisense orientation. That is, the DNA molecule isoperably linked with a regulatory sequence in a manner which allows forexpression (by transcription of the DNA molecule) of an RNA moleculewhich is antisense, relative to the mRNA encoding a polypeptide of theinvention. Regulatory sequences operably linked with a nucleic acidcloned in the antisense orientation can be selected which directcontinuous expression of the antisense RNA molecule in a variety of celltypes, for instance viral promoters and/or enhancers, or regulatorysequences can be selected which direct constitutive, tissue specific, orcell type specific expression of antisense RNA. The antisense expressionvector can be in the form of a recombinant plasmid, phagemid, orattenuated virus in which antisense nucleic acids are produced under thecontrol of a high efficiency regulatory region, the activity of whichcan be determined by the cell type into which the vector is introduced.For a discussion of the regulation of gene expression using antisensegenes see Weintraub et al. (Reviews—Trends in Genetics, Vol. 1(1) 1986).

[0949] Another aspect of the invention pertains to host cells into whicha recombinant expression vector of the invention has been introduced.The terms “host cell” and “recombinant host cell” are usedinterchangeably herein. It is understood that such terms refer not onlyto the particular subject cell but to the progeny or potential progenyof such a cell. Because certain modifications can occur in succeedinggenerations due to either mutation or environmental influences, suchprogeny may not, in fact, be identical to the parent cell, but are stillincluded within the scope of the term as used herein.

[0950] A host cell can be any prokaryotic (e.g., E. coli) or eukaryoticcell (e.g., insect cells, yeast or mammalian cells).

[0951] Vector DNA can be introduced into prokaryotic or eukaryotic cellsvia conventional transformation or transfection techniques. As usedherein, the terms “transformation” and “transfection” are intended torefer to a variety of art-recognized techniques for introducing foreignnucleic acid into a host cell, including calcium phosphate or calciumchloride co-precipitation, DEAE-dextran-mediated transfection,lipofection, and electroporation.

[0952] Suitable methods for transforming or transfecting host cells canbe found in Sambrook, et al. (supra), and other laboratory manuals.

[0953] For stable transfection of mammalian cells, it is known that,depending upon the expression vector and transfection technique used,only a small fraction of cells integrate the foreign DNA into theirgenome. In order to identify and select these integrants, a gene thatencodes a selectable marker (e.g., for resistance to antibiotics) can beintroduced into the host cells along with the gene of interest. Examplesof selectable markers include those which confer resistance to drugs,such as G418, hygromycin and methotrexate. Cells stably transfected withthe introduced nucleic acid can be identified by drug selection (e.g.,cells that have incorporated the selectable marker gene survive, whileother cells die).

[0954] A host cell of the invention, such as a prokaryotic or eukaryotichost cell in culture, can be used to produce a polypeptide of theinvention. Accordingly, the invention further provides methods forproducing a polypeptide of the invention using the host cells of theinvention. In one embodiment, the method comprises culturing the hostcell of invention (into which a recombinant expression vector encoding apolypeptide of the invention has been introduced) in a suitable mediumsuch that the polypeptide is produced. In another embodiment, the methodfurther comprises isolating the polypeptide from the medium or the hostcell.

[0955] The host cells of the invention can be used to produce non-humantransgenic animals. For example, in one embodiment, a host cell of theinvention is a fertilized oocyte or an embryonic stem cell into which asequences encoding a polypeptide of the invention have been introduced.Such host cells can then be used to create non-human transgenic animalsin which exogenous sequences encoding a polypeptide of the inventionhave been introduced into their genome or homologous recombinant animalsin which endogenous encoding a polypeptide of the invention sequenceshave been altered. Such animals are useful for studying the functionand/or activity of the polypeptide and for identifying and/or evaluatingmodulators of polypeptide activity. As used herein, a “transgenicanimal” is a non-human animal, preferably a mammal, more preferably arodent such as a rat or mouse, in which one or more of the cells of theanimal includes a transgene. Other examples of transgenic animalsinclude non-human primates, sheep, dogs, cows, goats, chickens,amphibians, etc. A transgene is exogenous DNA which is integrated intothe genome of a cell from which a transgenic animal develops and whichremains in the genome of the mature animal, thereby directing expressionof an encoded gene product in one or more cell types or tissues of thetransgenic animal. As used herein, an “homologous recombinant animal” isa non-human animal, preferably a mammal, more preferably a mouse, inwhich an endogenous gene has been altered by homologous recombinationbetween the endogenous gene and an exogenous DNA molecule introducedinto a cell of the animal, e.g., an embryonic cell of the animal, priorto development of the animal.

[0956] A transgenic animal of the invention can be created byintroducing a nucleic acid encoding a polypeptide of the invention (or ahomologue thereof) into the male pronuclei of a fertilized oocyte (e.g.,by microinjection or retroviral infection) and allowing the oocyte todevelop in a pseudopregnant female foster animal. Intronic sequences andpolyadenylation signals can also be included in the transgene toincrease the efficiency of expression of the transgene. Atissue-specific regulatory sequence(s) can be operably linked with thetransgene to direct expression of a polypeptide of the invention toparticular cells. Methods for generating transgenic animals via embryomanipulation and microinjection, particularly animals such as mice, havebecome conventional in the art and are described, for example, in U.S.Pat. Nos. 4,736,866 and 4,870,009, U.S. Pat. No. 4,873,191 and in Hogan,Manipulating the Mouse Embryo, (Cold Spring Harbor Laboratory Press,Cold Spring Harbor, N.Y., 1986). Similar methods are used for productionof other transgenic animals. A transgenic founder animal can beidentified based upon the presence of the transgene in its genomneand/or expression of mRNA encoding the transgene in tissues or cells ofthe animals. A transgenic founder animal can be used to breed additionalanimals carrying the transgene. Moreover, transgenic animals harboringthe transgene can further be bred to other transgenic animals harboringother transgenes.

[0957] To create an homologous recombinant animal, a vector is preparedwhich contains at least a portion of a gene encoding a polypeptide ofthe invention into which a deletion, addition or substitution has beenintroduced to thereby alter, e.g., functionally disrupt, the gene. Inone embodiment, the vector is designed such that, upon homologousrecombination, the endogenous gene is functionally disrupted (i.e., nolonger encodes a functional protein; also referred to as a “knock out”vector). Alternatively, the vector can be designed such that, uponhomologous recombination, the endogenous gene is mutated or otherwisealtered, but still encodes functional protein (e.g., the upstreamregulatory region can be altered to thereby alter the expression of theendogenous protein). In the homologous recombination vector, the alteredportion of the gene is flanked at its 5′ and 3′ ends by additionalnucleic acid of the gene to allow for homologous recombination to occurbetween the exogenous gene carried by the vector and an endogenous genein an embryonic stem cell. The additional flanking nucleic acidsequences are of sufficient length for successful homologousrecombination with the endogenous gene. Typically, several kilobases offlanking DNA (both at the 5′ and 3′ ends) are included in the vector(see, e.g., Thomas and Capecchi (1987) Cell 51:503 for a description ofhomologous recombination vectors). The vector is introduced into anembryonic stem cell line (e.g., by electroporation) and cells in whichthe introduced gene has homologously recombined with the endogenous geneare selected (see, e.g., Li et al. (1992) Cell 69:915). The selectedcells are then injected into a blastocyst of an animal (e.g., a mouse)to form aggregation chimeras (see, e.g., Bradley in Teratocarcinomas andEmbryonic Stem Cells: A Practical Approach, Robertson, ed. (IRL, Oxford,1987) pp. 1113-152). A chimeric embryo can then be implanted into asuitable pseudopregnant female foster animal and the embryo brought toterm. Progeny harboring the homologously recombined DNA in their germcells can be used to breed animals in which all cells of the animalcontain the homologously recombined DNA by germline transmission of thetransgene. Methods for constructing homologous recombination vectors andhomologous recombinant animals are described further in Bradley (1991)Current Opinion in Bio/Technology 2:823-829 and in PCT PublicationNumbers WO 90/11354, WO 91/01140, WO 92/0968, and WO 93/04169.

[0958] In another embodiment, transgenic non-human animals can beproduced which contain selected systems which allow for regulatedexpression of the transgene. One example of such a system is thecre/loxP recombinase system of bacteriophage P1. For a description ofthe cre/loxP recombinase system, see, e.g., Lakso et al. (1992) Proc.Natl. Acad. Sci. USA 89:6232-6236. Another example of a recombinasesystem is the FLP recombinase system of Saccharomyces cerevisiae(O'Gorman et al. (1991) Science 251:1351-1355. If a cre/loxP recombinasesystem is used to regulate expression of the transgene, animalscontaining transgenes encoding both the Cre recombinase and a selectedprotein are required. Such animals can be provided through theconstruction of “double” transgenic animals, e.g., by mating twotransgenic animals, one containing a transgene encoding a selectedprotein and the other containing a transgene encoding a recombinase.

[0959] Clones of the non-human transgenic animals described herein canbe produced according to the methods described in Wilmut et al. (1997)Nature 385:810-813 and PCT Publication Numbers WO 97/07668 and WO97/07669.

[0960] IV. Pharmaceutical Compositions

[0961] The nucleic acid molecules, polypeptides, and antibodies (alsoreferred to herein as “active compounds”) of the invention can beincorporated into pharmaceutical compositions suitable foradministration. Such compositions typically comprise the nucleic acidmolecule, protein, or antibody and a pharmaceutically acceptablecarrier. As used herein the language “pharmaceutically acceptablecarrier” is intended to include any and all solvents, dispersion media,coatings, anti-bacterial and anti-fungal agents, isotonic and absorptiondelaying agents, and the like, compatible with pharmaceuticaladministration. The use of such media and agents for pharmaceuticallyactive substances is well known in the art. Except insofar as anyconventional media or agent is incompatible with the active compound,use thereof in the compositions is contemplated. Supplementary activecompounds can also be incorporated into the compositions.

[0962] The invention includes methods for preparing pharmaceuticalcompositions for modulating the expression or activity of a polypeptideor nucleic acid of the invention. Such methods comprise formulating apharmaceutically acceptable carrier with an agent which modulatesexpression or activity of a polypeptide or nucleic acid of theinvention. Such compositions can further include additional activeagents. Thus, the invention further includes methods for preparing apharmaceutical composition by formulating a pharmaceutically acceptablecarrier with an agent which modulates expression or activity of apolypeptide or nucleic acid of the invention and one or more additionalactive compounds.

[0963] The agent which modulates expression or activity can, forexample, be a small molecule. For example, such small molecules includepeptides, peptidomimetics, amino acids, amino acid analogs,polynucleotides, polynucleotide analogs, nucleotides, nucleotideanalogs, organic or inorganic compounds (i.e., including heteroorganicand organometallic compounds) having a molecular weight less than about10,000 grams per mole, organic or inorganic compounds having a molecularweight less than about 5,000 grams per mole, organic or inorganiccompounds having a molecular weight less than about 1,000 grams permole, organic or inorganic compounds having a molecular weight less thanabout 500 grams per mole, and salts, esters, and other pharmaceuticallyacceptable forms of such compounds.

[0964] It is understood that appropriate doses of small molecule agentsand protein or polypeptide agents depends upon a number of factorswithin the ken of the ordinarily skilled physician, veterinarian, orresearcher. The dose(s) of these agents will vary, for example,depending upon the identity, size, and condition of the subject orsample being treated, further depending upon the route by which thecomposition is to be administered, if applicable, and the effect whichthe practitioner desires the agent to have upon the nucleic acid orpolypeptide of the invention. Examples of doses of a small moleculeinclude milligram or microgram amounts per kilogram of subject or sampleweight (e.g., about 1 microgram per kilogram to about 500 milligrams perkilogram, about 100 micrograms per kilogram to about 5 milligrams perkilogram, or about 1 microgram per kilogram to about 50 micrograms perkilogram). Examples of doses of a protein or polypeptide include gram,milligram or microgram amounts per kilogram of subject or sample weight(e.g., about 1 microgram per kilogram to about 5 grams per kilogram,about 100 micrograms per kilogram to about 500 milligrams per kilogram,or about 1 milligram per kilogram to about 50 milligrams per kilogram).For antibodies, examples of dosages are from about 0.1 milligram perkilogram to 100 milligrams per kilogram of body weight (generally 10milligrams per kilogram to 20 milligrams per kilogram). If the antibodyis to act in the brain, a dosage of 50 milligrams per kilogram to 100milligrams per kilogram is usually appropriate. It is furthermoreunderstood that appropriate doses of one of these agents depend upon thepotency of the agent with respect to the expression or activity to bemodulated. Such appropriate doses can be determined using the assaysdescribed herein. When one or more of these agents is to be administeredto an animal (e.g., a human) in order to modulate expression or activityof a polypeptide or nucleic acid of the invention, a physician,veterinarian, or researcher can, for example, prescribe a relatively lowdose at first, subsequently increasing the dose until an appropriateresponse is obtained. In addition, it is understood that the specificdose level for any particular animal subject will depend upon a varietyof factors including the activity of the specific agent employed, theage, body weight, general health, gender, and diet of the subject, thetime of administration, the route of administration, the rate ofexcretion, any drug combination, and the degree of expression oractivity to be modulated.

[0965] A pharmaceutical composition of the invention is formulated to becompatible with its intended route of administration. Examples of routesof administration include patenteral, e.g., intravenous, intradermal,subcutaneous, oral (e.g., inhalation), transdermal (topical),transmucosal, and rectal administration. Solutions or suspensions usedfor parenteral, intradermal, or subcutaneous application can include thefollowing components: a sterile diluent such as water for injection,saline solution, fixed oils, polyethylene glycols, glycerine, propyleneglycol or other synthetic solvents; antibacterial agents such as benzylalcohol or methyl parabens; antioxidants such as ascorbic acid or sodiumbisulfite; chelating agents such as ethylenediamine-tetraacetic acid;buffers such as acetates, citrates or phosphates; and agents for theadjustment of tonicity such as sodium chloride or dextrose. pH can beadjusted using acids or bases, such as hydrochloric acid or sodiumhydroxide. The parenteral preparation can be enclosed in ampules,disposable syringes or multiple dose vials made of glass or plastic.

[0966] Pharmaceutical compositions suitable for injectable use includesterile aqueous solutions (where water soluble) or dispersions andsterile powders for the extemporaneous preparation of sterile injectablesolutions or dispersions. For intravenous administration, suitablecarriers include physiological saline, bacteriostatic water, CREMOPHORT™EL (BASF; Parsippany, N.J.) or phosphate buffered saline (PBS). Thecomposition should be sterile and should be fluid to the extent thateasy syringability exists. It should be stable under the conditions ofmanufacture and storage and should be preserved against thecontaminating action of microorganisms such as bacteria and fungi. Thecarrier can be a solvent or dispersion medium containing, for example,water, ethanol, polyol (for example, glycerol, propylene glycol, andliquid polyethylene glycol, and the like), and suitable mixturesthereof. The proper fluidity can be maintained, for example, by the useof a coating such as lecithin, by the maintenance of the requiredparticle size in the case of dispersion and by the use of surfactants.Prevention of the action of microorganisms can be achieved by variousanti-bacterial and anti-fungal agents, for example, parabens,chlorobutanol, phenol, ascorbic acid, thimerosal, and the like. In manycases, it will be preferable to include isotonic agents, for example,sugars, polyalcohols such as mannitol, sorbitol, or sodium chloride inthe composition. Prolonged absorption of the injectable compositions canbe brought about by including in the composition an agent which delaysabsorption, for example, aluminum monostearate and gelatin.

[0967] Sterile injectable solutions can be prepared by incorporating theactive compound (e.g., a polypeptide or antibody) in the required amountin an appropriate solvent with one or a combination of ingredientsenumerated above, as required, followed by filtered sterilization.Generally, dispersions are prepared by incorporating the active compoundinto a sterile vehicle which contains a basic dispersion medium, andthen incorporating the required other ingredients from those enumeratedabove. In the case of sterile powders for the preparation of sterileinjectable solutions, examples of methods of preparation are vacuumdrying and freeze-drying which yields a powder of the active ingredientplus any additional desired ingredient from a previouslysterile-filtered solution thereof.

[0968] Oral compositions generally include an inert diluent or an ediblecarrier. They can be enclosed in gelatin capsules or compressed intotablets. For the purpose of oral therapeutic administration, the activecompound can be incorporated with excipients and used in the form oftablets, troches, or capsules. Oral compositions can also be preparedusing a fluid carrier for use as a mouthwash, wherein the compound inthe fluid carrier is applied orally and swished and expectorated orswallowed.

[0969] Pharmaceutically compatible binding agents, adjuvant materials,or both, can be included as part of the composition. The tablets, pills,capsules, troches, and the like can contain any of the followingingredients, or compounds of a similar nature: a binder such asmicrocrystalline cellulose, gum tragacanth or gelatin; an excipient suchas starch or lactose, a disintegrating agent such as alginic acid,PRIMOGEL™, or corn starch; a lubricant such as magnesium stearate orSterotes; a glidant such as colloidal silicon dioxide; a sweeteningagent such as sucrose or saccharin; or a flavoring agent such aspeppermint, methyl salicylate, or orange flavoring.

[0970] For administration by inhalation, the compounds are delivered inthe form of an aerosol spray from a pressurized container or dispenserwhich contains a suitable propellant, e.g., a gas such as carbondioxide, or a nebulizer.

[0971] Systemic administration can also be by transmucosal ortransdermal means. For transmucosal or transdermal administration,penetrants appropriate to the barrier to be permeated are used in theformulation. Such penetrants are generally known in the art, andinclude, for example, for transmucosal administration, detergents, bilesalts, and fusidic acid derivatives. Transmucosal administration can beaccomplished through the use of nasal sprays or suppositories. Fortransdermal administration, the active compounds are formulated intoointments, salves, gels, or creams as generally known in the art.

[0972] The compounds can also be prepared in the form of suppositories(e.g., with conventional suppository bases such as cocoa butter andother glycerides) or retention enemas for rectal delivery.

[0973] In one embodiment, the active compounds are prepared withcarriers that will protect the compound against rapid elimination fromthe body, such as a controlled release formulation, including implantand microencapsulated delivery systems. Biodegradable, biocompatiblepolymers can be used, such as ethylene vinyl acetate, polyanhydrides,polyglycolic acid, collagen, polyorthoesters, and polylactic acid.Methods for preparation of such formulations will be apparent to thoseskilled in the art. The materials can also be obtained commercially fromAlza Corporation and Nova Pharmaceuticals, Inc. Liposomal suspensions(including liposomes having monoclonal antibodies incorporated thereinor thereon) can also be used as pharmaceutically acceptable carriers.These can be prepared according to methods known to those skilled in theart, for example, as described in U.S. Pat. No. 4,522,811.

[0974] It is especially advantageous to formulate oral or parenteralcompositions in dosage unit form for ease of administration anduniformity of dosage. Dosage unit form as used herein refers tophysically discrete units suited as unitary dosages for the subject tobe treated; each unit containing a predetermined quantity of activecompound calculated to produce the desired therapeutic effect inassociation with the required pharmaceutical carrier. The specificationfor the dosage unit forms of the invention are dictated by and directlydependent on the unique characteristics of the active compound and theparticular therapeutic effect to be achieved, and the limitationsinherent in the art of compounding such an active compound for thetreatment of individuals.

[0975] Generally, partially human antibodies and fully human antibodieshave a longer half-life within the human body than other antibodies.Accordingly, lower dosages and less frequent administration is oftenpossible. Modifications such as lipidation can be used to stabilizeantibodies and to enhance uptake and tissue penetration (e.g., into thebrain). A method for lipidation of antibodies is described by Cruikshanket al. ((1997) J. Acquired Immune Deficiency Syndromes and HumanRetrovirology 14:193).

[0976] The nucleic acid molecules of the invention can be inserted intovectors and used as gene therapy vectors. Gene therapy vectors can bedelivered to a subject by, for example, intravenous injection, localadministration (U.S. Pat. No. 5,328,470), or by stereotactic injection(see, e.g., Chen et al. (1994) Proc. Natl. Acad. Sci. USA 91:3054-3057).The pharmaceutical preparation of the gene therapy vector can includethe gene therapy vector in an acceptable diluent, or can comprise a slowrelease matrix in which the gene delivery vehicle is imbedded.Alternatively, where the complete gene delivery vector can be producedintact from recombinant cells, e.g., retroviral vectors, thepharmaceutical preparation can include one or more cells which producethe gene delivery system.

[0977] It is recognized that the pharmaceutical compositions and methodsdescribed herein can be used independently or in combination with oneanother. That is, subjects can be administered one or more of thepharmaceutical compositions, e.g., pharmaceutical compositionscomprising a nucleic acid molecule or protein of the invention or amodulator thereof, subjected to one or more of the therapeutic methodsdescribed herein, or both, in temporally overlapping or non-overlappingregimens. When therapies overlap temporally, the therapies may generallyoccur in any order and can be simultaneous (e.g., administeredsimultaneously together in a composite composition or simultaneously butas separate compositions) or interspersed. By way of example, a subjectafflicted with a disorder described herein can be simultaneously orsequentially administered both a cytotoxic agent which selectively killsaberrant cells and an antibody (e.g., an antibody of the invention)which can, in one embodiment, be conjugated or linked with a therapeuticagent, a cytotoxic agent, an imaging agent, or the like.

[0978] The pharmaceutical compositions can be included in a container,pack, or dispenser together with instructions for administration.

[0979] V. Uses and Methods of the Invention

[0980] The nucleic acid molecules, proteins, protein homologs, andantibodies described herein can be used in one or more of the followingmethods: a) screening assays; b) detection assays (e.g., chromosomalmapping, tissue typing, forensic biology); c) predictive medicine (e.g.,diagnostic assays, prognostic assays, monitoring clinical trials, andpharmacogenomics); and d) methods of treatment (e.g., therapeutic andprophylactic). For example, polypeptides of the invention can to usedfor all of the purposes identified herein in portions of the disclosurerelating to individual types of protein of the invention. The isolatednucleic acid molecules of the invention can be used to express proteins(e.g., via a recombinant expression vector in a host cell in genetherapy applications), to detect mRNA (e.g., in a biological sample) ora genetic lesion, and to modulate activity of a polypeptide of theinvention. In addition, the polypeptides of the invention can be used toscreen drugs or compounds which modulate activity or expression of apolypeptide of the invention as well as to treat disorders characterizedby insufficient or excessive production of a protein of the invention orproduction of a form of a protein of the invention which has decreasedor aberrant activity compared to the wild type protein. In addition, theantibodies of the invention can be used to detect and isolate a proteinof the and modulate activity of a protein of the invention.

[0981] This invention further pertains to novel agents identified by theabove-described screening assays and uses thereof for treatments asdescribed herein.

[0982] A. Screening Assays

[0983] The invention provides a method (also referred to herein as a“screening assay”) for identifying modulators, i.e., candidate or testcompounds or agents (e.g., peptides, peptidomimetics, small molecules orother drugs) which bind with a polypeptide of the invention or have astimulatory or inhibitory effect on, for example, expression or activityof a polypeptide of the invention.

[0984] In one embodiment, the invention provides assays for screeningcandidate or test compounds which bind with or modulate the activity ofthe membrane-bound form of a polypeptide of the invention orbiologically active portion thereof. The test compounds of the presentinvention can be obtained using any of the numerous approaches incombinatorial library methods known in the art, including: biologicallibraries; spatially addressable parallel solid phase or solution phaselibraries; synthetic library methods requiring deconvolution; the“one-bead one-compound” library method; and synthetic library methodsusing affinity chromatography selection. The biological library approachis limited to peptide libraries, while the other four approaches areapplicable to peptide, non-peptide oligomer, or small molecule librariesof compounds (Lam (1997) Anticancer Drug Des. 12:145).

[0985] Examples of methods useful for the synthesis of molecularlibraries can be found in the art, for example in: DeWitt et al. (1993)Proc. Natl. Acad. Sci. USA 90:6909; Erb et al. (1994) Proc. Natl. Acad.Sci. USA 91:11422; Zuckermann et al. (1994). J. Med. Chem. 37:2678; Choet al. (1993) Science 261:1303; Carrell et al. (1994) Angew. Chem. Int.Ed.

[0986] Engl. 33:2059; Carell et al. (1994) Angew. Chem. Int. Ed. Engl.33:2061; and Gallop et al. (1994) J. Med. Chem. 37:1233.

[0987] Libraries of compounds can be presented in solution (e.g.,Houghten (1992) Bio/Techniques 13:412-421), or on beads (Lam (1991)Nature 354:82-84), chips (Fodor (1993) Nature 364:555-556), bacteria(U.S. Pat. No. 5,223,409), spores (U.S. Pat. Nos. 5,571,698; 5,403,484;and 5,223,409), plasmids (Cull et al. (1992) Proc. Natl. Acad. Sci. USA89:1865-1869) or phage (Scott and Smith (1990) Science 249:386-390;Devlin (1990) Science 249:404-406; Cwirla et al. (1990) Proc. Natl.Acad. Sci. USA 87:6378-6382; and Felici (1991) J. Mol. Biol.222:301-310).

[0988] In one embodiment, an assay is a cell-based assay in which a cellwhich expresses a membrane-bound form of a polypeptide of the invention,or a biologically active portion thereof, on the cell surface iscontacted with a test compound and the ability of the test compound tobind with the polypeptide is determined. The cell, for example, can be ayeast cell or a cell of mammalian origin. Determining the ability of thetest compound to bind with the polypeptide can be accomplished, forexample, by coupling the test compound with a radioisotope or enzymaticlabel such that binding of the test compound to the polypeptide orbiologically active portion thereof can be determined by detecting thelabeled compound in a complex. For example, test compounds can belabeled with ¹²⁵I, ³⁵S, ¹⁴C, or ³H, either directly or indirectly, andthe radioisotope detected by direct counting of radio-emission or byscintillation counting. Alternatively, test compounds can beenzymatically labeled with, for example, horseradish peroxidase,alkaline phosphatase, or luciferase, and the enzymatic label detected bydetermination of conversion of an appropriate substrate to product. Inone embodiment, the assay comprises contacting a cell which expresses amembrane-bound form of a polypeptide of the invention, or a biologicallyactive portion thereof, on the cell surface with a known compound whichbinds the polypeptide to form an assay mixture, contacting the assaymixture with a test compound, and determining the ability of the testcompound to interact with the polypeptide, wherein determining theability of the test compound to interact with the polypeptide comprisesdetermining the ability of the test compound to preferentially bind withthe polypeptide or a biologically active portion thereof as compared tothe known compound.

[0989] In another embodiment, the assay involves assessment of anactivity characteristic of the polypeptide, wherein binding of the testcompound with the polypeptide or a biologically active portion thereofalters (i.e., increases or decreases) the activity of the polypeptide.

[0990] In another embodiment, an assay is a cell-based assay comprisingcontacting a cell expressing a membrane-bound form of a polypeptide ofthe invention, or a biologically active portion thereof, on the cellsurface with a test compound and determining the ability of the testcompound to modulate (e.g., stimulate or inhibit) the activity of thepolypeptide or biologically active portion thereof. Determining theability of the test compound to modulate the activity of the polypeptideor a biologically active portion thereof can be accomplished, forexample, by determining the ability of the polypeptide to bind with orinteract with a target molecule or to transport molecules across thecytoplasmic membrane.

[0991] Determining the ability of a polypeptide of the invention to bindwith or interact with a target molecule can be accomplished by one ofthe methods described above for determining direct binding. As usedherein, a “target molecule” is a molecule with which a selectedpolypeptide (e.g., a polypeptide of the invention binds or interactswith in nature, for example, a molecule on the surface of a cell whichexpresses the selected protein, a molecule on the surface of a secondcell, a molecule in the extracellular milieu, a molecule associated withthe internal surface of a cell membrane or a cytoplasmic molecule. Atarget molecule can be a polypeptide of the invention or some otherpolypeptide or protein. For example, a target molecule can be acomponent of a signal transduction pathway which facilitatestransduction of an extracellular signal (e.g., a signal generated bybinding of a compound to a polypeptide of the invention) through thecell membrane and into the cell or a second intercellular protein whichhas catalytic activity or a protein which facilitates association ofdownstream signaling molecules with a polypeptide of the invention.Determining the ability of a polypeptide of the invention to bind withor interact with a target molecule can be accomplished by determiningthe activity of the target molecule. For example, the activity of thetarget molecule can be determined by detecting induction of a cellularsecond messenger of the target (e.g., an mRNA, intracellular Ca²⁺,diacylglycerol, IP3, and the like), detecting catalytic/enzymaticactivity of the target on an appropriate substrate, detecting inductionof a reporter gene (e.g., a regulatory element that is responsive to apolypeptide of the invention operably linked with a nucleic acidencoding a detectable marker, e.g., luciferase), or detecting a cellularresponse, for example, cellular differentiation, or cell proliferation.

[0992] In yet another embodiment, an assay of the present invention is acell-free assay comprising contacting a polypeptide of the invention orbiologically active portion thereof with a test compound and determiningthe ability of the test compound to bind with the polypeptide orbiologically active portion thereof. Binding of the test compound withthe polypeptide can be determined either directly or indirectly asdescribed above. In one embodiment, the assay includes contacting thepolypeptide of the invention or biologically active portion thereof witha known compound which binds the polypeptide to form an assay mixture,contacting the assay mixture with a test compound, and determining theability of the test compound to interact with the polypeptide, whereindetermining the ability of the test compound to interact with thepolypeptide comprises determining the ability of the test compound topreferentially bind with the polypeptide or biologically active portionthereof as compared to the known compound.

[0993] In another embodiment, an assay is a cell-free assay comprisingcontacting a polypeptide of the invention or biologically active portionthereof with a test compound and determining the ability of the testcompound to modulate (e.g., stimulate or inhibit) the activity of thepolypeptide or biologically active portion thereof. Determining theability of the test compound to modulate activity of the polypeptide canbe accomplished, for example, by determining the ability of thepolypeptide to bind with a target molecule by one of the methodsdescribed above for determining direct binding. In an alternativeembodiment, determining the ability of the test compound to modulate theactivity of the polypeptide can be accomplished by determining theability of the polypeptide of the invention to further modulate thetarget molecule. For example, the catalytic activity, the enzymaticactivity, or both, of the target molecule on an appropriate substratecan be determined as previously described.

[0994] In yet another embodiment, the cell-free assay comprisescontacting a polypeptide of the invention or biologically active portionthereof with a known compound which binds the polypeptide to form anassay mixture, contacting the assay mixture with a test compound, anddetermining the ability of the test compound to interact with thepolypeptide. Ability of the test compound to interact with thepolypeptide can be determined by assessing the ability of thepolypeptide to preferentially bind with or modulate the activity of atarget molecule, or by any other method.

[0995] The cell-free assays of the present invention are amenable to useof either soluble or membrane-bound forms (where applicable) of apolypeptide of the invention. In the case of cell-free assays comprisinga membrane-bound form of the polypeptide, it can be desirable to use asolubilizing agent in order to maintain the membrane-bound form of thepolypeptide in solution. Examples of such solubilizing agents includenon-ionic detergents such as n-octylglucoside, n-dodecylglucoside,n-octylmaltoside, octanoyl-N-methylglucamide,decanoyl-N-methylglucamide, Triton X-100, Triton X-114, Thesit,isotridecypoly(ethylene glycol ether)n, 3-{(3-cholamidopropyl)dimethylamminio}-1-propane sulfonate (CHAPS), 3-{(3-cholamidopropyl)dimethylamminio}-2-hydroxy-1-propane sulfonate (CHAPSO), orN-dodecyl-N,N-dimethyl-3-ammonio-1-propane sulfonate.

[0996] In one or more embodiments of the above assay methods of thepresent invention, it can be desirable to immobilize either thepolypeptide of the invention or its target molecule in order tofacilitate separation of complexed and non-complexed forms of one orboth of the molecules, as well as to accommodate automation of theassay. Binding of a test compound with the polypeptide, or interactionof the polypeptide with a target molecule in the presence and absence ofa candidate compound, can be accomplished in any vessel suitable forcontaining the reactants. Examples of such vessels include microtiterplates, test tubes, and micro-centrifuge tubes. In one embodiment, afusion protein can be provided which adds a domain that allows one orboth of the proteins to be bound to a matrix. For example,glutathione-S-transferase fusion proteins or glutathione-S-transferasefusion proteins can be adsorbed onto glutathione SEPHAROSE™ beads (SigmaChemical; St. Louis, Mo.) or glutathione-derivatized microtiter plates,which are combined with the test compound and either the non-adsorbedtarget protein or a polypeptide of the invention. The combination isincubated under conditions conducive to complex formation (e.g., atphysiological conditions for salt and pH). Following incubation, thebeads or microtiter plate wells are washed to remove unbound components,and complex formation is measured directly or indirectly, for example,as described above. Alternatively, the complexes can be dissociated fromthe matrix, and the level of binding or activity of the polypeptide ofthe invention can be determined using standard techniques, such as thosedescribed herein.

[0997] Other techniques for immobilizing proteins on matrices can alsobe used in the screening assays of the invention. For example, eitherthe polypeptide of the invention or a target molecule thereof (e.g., aprotein which binds therewith or a substrate or an analog of a substrateof the protein of the invention) can be immobilized using conjugation ofbiotin and streptavidin. Biotinylated polypeptide of the invention ortarget molecules can be prepared using biotin-NHS(biotin-N-hydroxy-succinimide) using techniques well known in the art(e.g., using a commercially available kit such as the biotinylation kitmanufactured by Pierce Chemical Co.; Rockford, Ill.), and immobilized inthe wells of streptavidin-coated 96-well plates (Pierce Chemical).Alternatively, antibodies which are reactive with the polypeptide of theinvention or target molecules but which do not interfere with binding ofthe polypeptide of the invention with its target molecule can bederivatized to the wells of the plate, and unbound target or polypeptideof the invention can be trapped in the wells by antibody conjugation.Methods for detecting such complexes, in addition to those describedabove for the GST-immobilized complexes, include immunodetection ofcomplexes using antibodies reactive with the polypeptide of theinvention or target molecule, as well as enzyme-linked assays which relyon detecting an enzymatic activity associated with the polypeptide ofthe invention or target molecule.

[0998] In another embodiment, modulators of expression of a polypeptideof the invention are identified in a method in which a cell is contactedwith a candidate compound and expression of the selected mRNA or protein(i.e., mRNA or protein corresponding to a polypeptide or nucleic acid ofthe invention) in the cell is determined. The level of expression of theselected mRNA or protein in the presence of the candidate compound iscompared with the level of expression of the selected mRNA or protein inthe absence of the candidate compound. The candidate compound can thenbe identified as a modulator of expression of the polypeptide of theinvention based on this comparison. For example, if expression of theselected mRNA or protein is greater (i.e., statistically significantlygreater) in the presence of the candidate compound than in its absence,then the candidate compound is identified as a stimulator of expressionof the selected mRNA or protein. Alternatively, if expression of theselected mRNA or protein is less (i.e., statistically significantlyless) in the presence of the candidate compound than in its absence,then the candidate compound is identified as an inhibitor of expressionof the selected mRNA or protein. The level of the selected mRNA orprotein expression in the cells can be determined by methods describedherein.

[0999] In yet another aspect of the invention, a polypeptide of theinvention can be used as a “bait protein” in a two-hybrid assay or threehybrid assay (see, e.g., U.S. Pat. No. 5,283,317; Zervos et al. (1993)Cell 72:223-232; Madura et al. (1993) J. Biol. Chem. 268:12046-12054;Bartel et al. (1993) Bio/Techniques 14:920-924; Iwabuchi et-al. (1993)Oncogene 8:1693-1696; and PCT Publication No. WO 94/10300), to identifyother proteins which bind with or interact with the polypeptide of theinvention and modulate activity of the polypeptide of the invention.Such binding proteins are also likely to be involved in the propagationof signals by the polypeptide of the inventions as, for example,upstream or downstream elements of a signaling pathway involving thepolypeptide of the invention.

[1000] This invention further pertains to novel agents identified by theabove-described screening assays and uses thereof for treatments asdescribed herein.

[1001] B. Detection Assays

[1002] Portions or fragments of the cDNA sequences identified herein(and the corresponding complete gene sequences) can be used in numerousways as polynucleotide reagents. For example, these sequences can beused to: (i) map their respective genes on a chromosome and, thus,locate gene regions associated with genetic disease; (ii) identify anindividual from a minute biological sample (tissue typing); and (iii)aid in forensic identification of a biological sample. Theseapplications are described in the subsections below.

[1003] 1. Chromosome Mapping

[1004] Once the sequence (or a portion of the sequence) of a gene hasbeen isolated, this sequence can be used to map the location of the geneon a chromosome. Accordingly, nucleic acid molecules described herein orfragments thereof, can be used to map the location of the correspondinggenes on a chromosome. Mapping of sequences to chromosomes is animportant first step in correlating these sequences with genesassociated with occurrence of disease. For example, the TANGO 457 genemaps to human chromosome 11p14.3; the TANGO 416 gene maps to humanchromosome 4 between chromosomal markers D4S422 and D4S1576; theINTERCEPT 400 gene maps to human chromosome 4 between markers D4S 1616and D4S 1611; the TANGO 331 gene maps to human chromosome 22 at22q11-q13, between markers WI-4572 and WI-8917; the TANGO 265 gene mapsto human chromosome 1 between markers D1S305 and D1S2635; and the TANGO286 gene maps to human chromosome 22 at 22q12-13.

[1005] Briefly, genes can be mapped to chromosomes by preparing PCRprimers (preferably 15-25 nucleotide residues in length) from thesequence of a gene of the invention. Computer analysis of the sequenceof a gene of the invention can be used to rapidly select primers that donot span more than one exon in the genomic DNA, which would complicatethe amplification process. These primers can be used for PCR screeningof somatic cell hybrids containing individual human chromosomes. Onlythose hybrids containing the human gene corresponding to the genesequences will yield an amplified fragment. For a review of thistechnique, see D'Eustachio et al. ((1983) Science 220:919-924).

[1006] PCR mapping of somatic cell hybrids is a rapid procedure forassigning a particular sequence to a particular chromosome. Three ormore sequences can be assigned per day using a single thermal cycler.Using one or more nucleic acid sequences of the invention to designoligonucleotide primers, sub-localization can be achieved using panelsof fragments prepared from specific chromosomes. Other mappingstrategies which can similarly be used to map a gene to its chromosomallocation include in situ hybridization (described in Fan et al. (1990)Proc. Natl. Acad. Sci. USA 87:6223-27), pre-screening with labeledflow-sorted chromosomes, and pre-selection by hybridization withchromosome specific cDNA libraries. Fluorescence in situ hybridization(FISH) of a DNA sequence using a metaphase chromosomal spread can beused to provide a precise chromosomal location in one step. For a reviewof this technique, see Verma et al. (Human Chromosomes: A Manual ofBasic Techniques (Pergamon Press, New York, 1988)).

[1007] Reagents for chromosome mapping can be used individually to marka single chromosome or a single site on a chromosome. Alternatively,panels of reagents can be used for marking multiple sites, multiplechromosomes, or both. Reagents corresponding to non-coding regions ofthe genes actually are preferred for mapping purposes. Coding sequencesare more likely to be conserved within gene families, thus increasingthe chance of cross-hybridization during chromosomal mapping.

[1008] Once a sequence has been mapped to a precise chromosomallocation, the physical position of the sequence on the chromosome can becorrelated with genetic map data. (Such data are found, for example, inV. McKusick, Mendelian Inheritance in Man, available on-line throughJohns Hopkins University Welch Medical Library). The relationshipbetween genes and disease, mapped to the same chromosomal region, canthen be identified by linkage analysis (co-inheritance of physicallyadjacent genes), described in, e.g., Egeland et al. (1987) Nature325:783-787.

[1009] Moreover, differences in the DNA sequences between individualsaffected and non-affected with a disease associated with a gene of theinvention can be determined. If a mutation is observed in some or all ofthe affected individuals, but not in any (or in very few) non-affectedindividuals, then the mutation is likely to be the causative agent ofthe particular disease. Comparison of affected and non-affectedindividuals generally involves first looking for structural alterationsin the chromosomes such as deletions or translocations that are visiblefrom chromosome spreads or detectable using PCR based on that DNAsequence. Ultimately, complete sequencing of genes from severalindividuals can be performed to confirm the presence of a mutation andto distinguish mutations from polymorphisms.

[1010] 2. Tissue Typing

[1011] The nucleic acid sequences of the present invention can also beused to identify individuals from minute biological samples. The UnitedStates military, for example, is considering the use of restrictionfragment length polymorphism (RFLP) for identification of its personnel.In this technique, an individual's genomic DNA is digested with one ormore restriction enzymes, and probed on a Southern blot to yield uniquebands for identification. This method does not suffer from the currentlimitations of physical identification devices such as general issue“dog tags,” which can be lost, switched, or stolen, making positiveidentification difficult. The sequences of the present invention areuseful as additional DNA markers for RFLP (described in U.S. Pat. No.5,272,057).

[1012] Furthermore, the sequences of the present invention can be usedto provide an alternative technique which determines the actualbase-by-base DNA sequence of selected portions of an individual'sgenome. The nucleic acid sequences described herein can be used toprepare two PCR primers from the 5′ and 3′ ends of the sequences. Theseprimers can then be used to amplify an individual's DNA and tosubsequently sequence it.

[1013] Panels of corresponding DNA sequences from individuals, preparedin this manner, can provide unique individual identifications, because(with the exception of identical twins) every individual has a uniqueset of such DNA sequences owing, at least in part, to allelicdifferences. Sequences of the present invention can be used to obtainsuch identification sequences from individuals and from tissue. Thenucleic acid sequences of the invention uniquely represent portions ofthe human genome. Allelic variation occurs to some degree in the codingregions of these sequences, and to a greater degree in the non-codingregions. It is estimated that allelic variation between individualhumans occurs with a frequency of about once per 500 nucleotideresidues. Each of the sequences described herein can, to some degree, beused as a standard against which DNA from an individual can be comparedfor identification purposes. Because greater numbers of polymorphismsoccur in the non-coding regions, fewer non-coding sequences arenecessary to differentiate individuals. The non-coding sequences of anyof SEQ ID NOs: 1, 31, 51, 71, 81, 91, 96, 101, 106, 111, 121, 141, 151,171, 181, 191, 201, 215, 221, 241, 251, 271, 279, 303, 308, 324, 329,351, 371, 379, 387, 403, 415, 423, and 437 can comfortably providepositive individual identification with a panel of perhaps 10 to 1,000primers which each yield a non-coding amplified sequence of 100 bases.If predicted coding sequences, such as those in any of SEQ ID NOs: 2,32, 52, 72, 82, 92, 97, 102, 107, 112, 122, 142, 152, 162, 172, 182,192, 202, 215, 222, 242, 252, 272, 280, 304, 309, 325, 330, 352, 362,372, 380, 388, 404, 416, 424, and 438are used, a more appropriate numberof primers for positive individual identification would be 500-2,000.

[1014] If a panel of reagents from the nucleic acid sequences describedherein is used to generate a unique identification database for anindividual, those same reagents can later be used to identify nucleicacids, cells, or tissue from that individual. Using the uniqueidentification database, positive identification of the individual,living or dead, can be made from extremely small samples.

[1015] 3. Use of Partial Gene Sequences in Forensic Biology

[1016] DNA-based identification techniques can be used in forensicbiology. Forensic biology is a scientific field employing genetic typingof biological evidence found at a crime scene as a means for positivelyidentifying, for example, a perpetrator of a crime. To make such anidentification, PCR technology can be used to amplify DNA sequencestaken from very small biological samples such as tissues (e.g., hair orskin) or body fluids (e.g., blood, saliva, or semen) found at a crimescene. The amplified sequence can be compared with a standard, therebyallowing identification of the origin of the biological sample.

[1017] The sequences of the present invention can be used to providepolynucleotide reagents (e.g., PCR primers) targeted to specific loci inthe human genome, which can enhance the reliability of DNA-basedforensic identifications by, for example, providing another“identification marker” (i.e., another DNA sequence that is unique to aparticular individual). As mentioned above, actual nucleotide sequenceinformation can be used for identification as an accurate alternative topatterns formed by restriction enzyme-generated fragments. Sequences ofnon-coding regions are particularly appropriate for this use, becausegreater numbers of polymorphisms occur in non-coding regions, making iteasier to differentiate individuals using this technique. Examples ofpolynucleotide reagents include the nucleic acid sequences of theinvention or portions thereof, e.g., fragments derived from non-codingregions having a length of at least 20 or 30 nucleotide residues.

[1018] The nucleic acid sequences described herein can further be usedto provide polynucleotide reagents, e.g., labeled or labelable probeswhich can be used in, for example, an in situ hybridization technique,to identify a specific tissue, e.g., brain tissue. This can be veryuseful in cases where a forensic pathologist is presented with a tissueof unknown origin. Panels of such probes can be used to identify tissueby species and/or by organ type.

[1019] C. Predictive Medicine

[1020] The present invention also pertains to the field of predictivemedicine in which diagnostic assays, prognostic assays, and monitoringclinical trials are used for prognostic (predictive) purposes to therebytreat an individual prophylactically. Accordingly, one aspect of thepresent invention relates to diagnostic assays for determiningexpression of a gene encoding a polypeptide of the invention as well asactivity of a polypeptide of the invention, in the context of abiological sample (e.g., blood, serum, cells, tissue) to therebydetermine whether an individual is afflicted with a disease or disorder,or is at risk of developing a disorder, associated with aberrant orunwanted expression of a gene encoding a polypeptide of the invention oraberrant or unwanted activity of a polypeptide of the invention. Theinvention also provides for prognostic (or predictive) assays fordetermining whether an individual is at risk of developing a disorderassociated with a protein of the invention, with expression of a nucleicacid encoding a polypeptide of the invention, or with activity of apolypeptide of the invention. For example, mutations in a gene encodinga polypeptide of the invention can be assayed in a biological sample.Such assays can be used for prognostic or predictive purpose to therebyprophylactically treat an individual prior to the onset of a disordercharacterized by or associated with a polypeptide of the invention,expression of a nucleic acid encoding it, or its activity.

[1021] As an alternative to making determinations based on the absoluteexpression level of selected genes, determinations may be based on thenormalized expression levels of these genes. Expression levels arenormalized by correcting the absolute expression level of a geneencoding a polypeptide of the invention by comparing its expression tothe expression of a different gene, e.g., a housekeeping gene that isconstitutively expressed. Suitable genes for normalization includehousekeeping genes such as the actin gene. This normalization allows thecomparison of the expression level in one sample (e.g., a patientsample), to another sample, or between samples from different sources.

[1022] Alternatively, the expression level can be provided as a relativeexpression level. To determine a relative expression level of a gene,the level of expression of the gene is determined for 10 or more samplesof different endothelial (e.g. intestinal endothelium, airwayendothelium, or other mucosal epithelium) cell isolates, preferably 50or more samples, prior to the determination of the expression level forthe sample in question. The mean expression level of each of the genesassayed in the larger number of samples is determined and this is usedas a baseline expression level for the gene(s) in question. Theexpression level of the gene determined for the test sample (absolutelevel of expression) is then divided by the mean expression valueobtained for that gene. This provides a relative expression level andaids in identifying extreme cases of disorders associated with aberrantexpression of a gene encoding a polypeptide of the invention protein orwith aberrant expression of a ligand thereof.

[1023] Preferably, the samples used in the baseline determination willbe from either or both of cells which aberrantly express a gene encodinga polypeptide of the invention or a ligand thereof (i.e. ‘diseasedcells’) and cells which express a gene encoding a polypeptide of theinvention at a normal level or a ligand thereof (i.e. ‘normal’ cells).The choice of the cell source is dependent on the use of the relativeexpression level. Using expression found in normal tissues as a meanexpression score aids in validating whether aberrance in expression of agene encoding a polypeptide of the invention occurs specifically indiseased cells. Such a use is particularly important in identifyingwhether a gene encoding a polypeptide of the invention can serve as atarget gene. In addition, as more data is accumulated, the meanexpression value can be revised, providing improved relative expressionvalues based on accumulated data. Expression data from endothelial cells(e.g. mucosal endothelial cells) provides a means for grading theseverity of the disorder.

[1024] Another aspect of the invention pertains to monitoring theinfluence of agents (e.g., drugs, antibodies, antisenseoligonucleotides, or other compounds) on the expression or activity of apolypeptide of the invention in clinical trials.

[1025] These and other agents are described in further detail in thefollowing sections.

[1026] 1. Diagnostic Assays

[1027] An example of a method for detecting the presence or absence of apolypeptide or nucleic acid of the invention in a biological sampleinvolves obtaining a biological sample from a test subject andcontaining the biological sample with a compound or an agent capable ofdetecting a polypeptide or nucleic acid (e.g., mRNA, genomic DNA) of theinvention. An example of an agent for detecting mRNA or genomic DNAencoding a polypeptide of the invention is a labeled nucleic acid probecapable of hybridizing with mRNA or genomic DNA encoding a polypeptideof the invention. The nucleic acid probe can be, for example, afull-length cDNA, such as the nucleic acid of one of SEQ ID NOs: 1, 31,51, 71, 81, 91, 96, 101, 106, 111, 121, 141, 151, 171, 181, 191, 201,217, 221, 241, 251, 271, 279, 303, 308, 324, 329, 351, 371, 379, 387,403, 415, 423, and 437, or a portion thereof, such as an oligonucleotideof at least 15, 30, 50, 100, 250 or 500 nucleotides in length andsufficient to specifically hybridize under stringent conditions with amRNA or genomic DNA encoding a polypeptide of the invention. Othersuitable probes for use in the diagnostic assays of the invention aredescribed herein.

[1028] An example of an agent for detecting a polypeptide of theinvention is an antibody capable of binding with a polypeptide of theinvention, such as an antibody having a detectable label. Antibodies canbe polyclonal or, preferably, monoclonal. An intact antibody, or afragment thereof (e.g., Fab or F(ab′)₂) can be used. The term “labeled,”with regard to the probe or antibody, includes direct labeling of theprobe or antibody by coupling (i.e., physically linking) a detectablesubstance to the probe or antibody, as well as indirect labeling of theprobe or antibody by coupling it with another reagent that is directlylabeled. Examples of indirect labeling include detection of a primaryantibody using a fluorescently labeled secondary antibody andend-labeling of a DNA probe with biotin such that it can be detectedwith fluorescently labeled streptavidin. The term “biological sample” isintended to include tissues, cells, and biological fluids isolated froma subject, as well as tissues, cells, and fluids present within asubject. That is, the detection method of the invention can be used todetect mRNA, protein, or genomic DNA in a biological sample in vitro aswell as in vivo. For example, in vitro techniques for detection of mRNAinclude Northern hybridization methods and in situ hybridizationmethods. In vitro techniques for detection of a polypeptide of theinvention include enzyme linked immunosorbent assays (ELISAs), Westernblots, immunoprecipitation, and immunofluorescence. In vitro techniquesfor detection of genomic DNA include Southern hybridizations.Furthermore, in vivo techniques for detection of a polypeptide of theinvention include introducing into a subject a labeled antibody directedagainst the polypeptide. For example, the antibody can be labeled with aradioactive marker, the presence and location of which in a subject canbe detected using standard imaging techniques.

[1029] In one embodiment, the biological sample contains proteinmolecules obtained from the test subject. Alternatively, the biologicalsample can contain mRNA molecules obtained from the test subject orgenomic DNA molecules obtained from the test subject. An example of abiological sample is a peripheral blood leukocyte-containing sampleobtained by conventional means from a subject (e.g., isolated peripheralblood leukocytes).

[1030] In another embodiment, the methods further involve obtaining acontrol biological sample from a control (i.e., non-afflicted) subject,contacting the control sample with a compound or agent capable ofdetecting a polypeptide of the invention or mRNA or genomic DNA encodinga polypeptide of the invention. The presence or amount of thepolypeptide, mRNA, or genomic DNA encoding the polypeptide in thecontrol and test samples can be compared t6 assess the degree, if any,to which the presence or amount in the test sample differs from that inthe control sample.

[1031] The invention also encompasses kits for detecting the presence ofa polypeptide or nucleic acid of the invention in a biological sampleobtained from a subject. Such kits can be used to determine if a subjectis suffering from or is at increased risk of developing a disorderassociated with aberrant expression of a polypeptide of the invention(e.g., one of the disorders described in the section of this disclosurewherein the individual polypeptide of the invention is discussed). Forexample, the kit can comprise a labeled compound or agent capable ofdetecting the polypeptide or mRNA encoding the polypeptide in abiological sample. The kit can also, or alternatively, contain means fordetermining the amount of the polypeptide or mRNA in the sample (e.g.,an antibody which specifically binds with the polypeptide or anoligonucleotide probe which binds with a nucleic acid encoding thepolypeptide). Kits can include instructions for assessing whether thetested subject is suffering from or is at risk of developing a disorderassociated with aberrant expression of the polypeptide if the amount ofthe polypeptide or mRNA encoding the polypeptide is above or below anormal level.

[1032] For antibody-based kits, the kit can comprise, for example: (1) afirst antibody (e.g., attached to a solid support) which specificallybinds with a polypeptide of the invention; and, optionally, (2) asecond, different antibody which specifically binds with either thepolypeptide or the first antibody and is conjugated with a detectableagent.

[1033] For oligonucleotide-based kits, the kit can comprise, forexample: (1) an oligonucleotide (e.g., a detectably labeledoligonucleotide) which hybridizes with a nucleic acid encoding apolypeptide of the invention or (2) a pair of primers useful foramplifying a nucleic acid encoding a polypeptide of the invention. Thekit can comprise, for example, a buffering agent, a preservative, or aprotein stabilizing agent. The kit can also comprise componentsnecessary for detecting the detectable agent (e.g., an enzyme or asubstrate). The kit can contain a control sample or a series of controlsamples which can be assayed and compared with the test sample assayresults. Each component of the kit can be enclosed within an individualcontainer and all of the various containers can furthermore be within asingle package, optionally with instructions for assessing whether thetested subject is suffering from or is at risk of developing a disorderassociated with aberrant expression of the polypeptide.

[1034] 2. Prognostic Assays

[1035] The methods described herein can furthermore be used asdiagnostic or prognostic assays to identify subjects having or at riskof developing a disease or disorder associated with aberrant expressionor activity of a polypeptide of the invention (e.g., one of thedisorders described in the section of this disclosure wherein theindividual polypeptide of the invention is discussed). Thus, the presentinvention provides a method in which a test sample is obtained from asubject and a polypeptide or nucleic acid (e.g., mRNA, genomic DNA) ofthe invention is detected, wherein the presence, level, or activity ofthe polypeptide or nucleic acid in the sample is associated with anenhanced or diminished risk of developing a disease or disorderassociated with aberrant expression or activity of the polypeptide.

[1036] Furthermore, the prognostic assays described herein can be usedto determine whether an agent (e.g., an agonist, antagonist,peptidomimetic, protein, peptide, nucleic acid, small molecule, or otherdrug candidate) can be administered to a subject in order to treat adisease or disorder associated with aberrant expression or activity of apolypeptide of the invention. For example, such methods can be used todetermine whether a subject can be effectively treated using a specificagent or class of agents (e.g., agents of a type which decrease activityof the polypeptide). Thus, the present invention provides methods fordetermining whether an agent can be administered to a subject in orderto effectively treat a disorder associated with aberrant expression oractivity of a polypeptide of the invention. When efficacious agents areknown or found, such assays can also be used to estimate tan efficaciousdose of the agent.

[1037] The methods of the invention can be used to detect geneticlesions or mutations in a gene of the invention in order to assess if asubject having the lesioned or mutated gene is at risk for a disordercharacterized aberrant expression or activity of a polypeptide of theinvention. In certain embodiments, the methods include detecting, in asample of cells obtained from the subject, the presence or absence of agenetic lesion or mutation characterized by at least one of analteration affecting the integrity of a gene encoding the polypeptide ofthe invention, or the mis-expression of the gene encoding thepolypeptide of the invention. For example, such genetic lesions ormutations can be detected by ascertaining the existence of at least oneof: 1) a deletion of one or more nucleotides from the gene; 2) anaddition of one or more nucleotides to the gene; 3) a substitution ofone or more nucleotides of the gene; 4) a chromosomal rearrangement ofthe gene; 5) an alteration in the level of a messenger RNA transcript ofthe gene; 6) an aberrant modification of the gene, such as of themethylation pattern of the genomic DNA; 7) a non-wild type splicingpattern of a messenger RNA transcript of the gene; 8) a non-wild typelevel of the protein encoded by the gene; 9) an allelic loss of thegene; and 10) an inappropriate post-translational modification of theprotein encoded by the gene. As described herein, there are a largenumber of assay techniques known in the art which can be used fordetecting such lesions and mutations in a gene.

[1038] In certain embodiments, detection of the lesion involves the useof an oligonucleotide primer in a polymerase chain reaction (PCR; see,e.g., U.S. Pat. Nos. 4,683,195 and 4,683,202), such as anchor PCR orRACE PCR, or, alternatively, in a ligation chain reaction (LCR; see,e.g., Landegran et al. (1988) Science 241:1077-1080; and Nakazawa et al.(1994) Proc. Natl. Acad. Sci. USA 91:360-364), the latter of which canbe particularly useful for detecting point mutations in a gene (see,e.g., Abravaya et al. (1995) Nucleic Acids Res. 23:675-682). This methodcan include the steps of collecting a sample of cells from a patient,isolating nucleic acid (e.g., genomic, mRNA, or both) from the cells ofthe sample, contacting the nucleic acid sample with one or more primerswhich specifically hybridize with the selected gene under conditionssuch that hybridization and amplification of the gene (if present)occurs, and detecting the presence or absence of an amplificationproduct. The method can also include detecting the size of theamplification product and comparing the length to the length of acorresponding product obtained in the same manner from a control sample.PCR, LCR, or both can be used as a preliminary amplification step inconjunction with any of the techniques used for detecting mutationsdescribed herein.

[1039] Alternative amplification methods include: self-sustainedsequence replication (Guatelli et al. (1990) Proc. Natl. Acad. Sci. USA87:1874-1878), transcriptional amplification system (Kwoh, et al. (1989)Proc. Natl. Acad. Sci. USA 86:1173-1177), Q-Beta Replicase (Lizardi etal. (1988) Bio/Technology 6:1197), or any other nucleic acidamplification method, followed by the detection of the amplifiedmolecules using any of a variety of techniques well known to those ofskill in the art. These detection schemes are especially useful fordetection of nucleic acid molecules if such molecules are present invery low numbers.

[1040] In an alternative embodiment, mutations in a selected gene can beidentified in a sample by detecting alterations in restriction enzymecleavage patterns. For example, sample and control DNA is isolated,(optionally) amplified, digested with one or more restrictionendonucleases, and fragment length sizes are determined by gelelectrophoresis and compared. Differences in fragment length sizesbetween sample and control DNA indicates occurrence of mutations orother sequence differences in the sample DNA. Moreover, sequencespecific ribozymes (see, e.g., U.S. Pat. No. 5,498,531) can be used toscore for the presence of specific mutations by development or loss of aribozyme cleavage site.

[1041] In other embodiments, genetic mutations are identified byhybridizing a sample and control nucleic acids, e.g., DNA or RNA, withhigh density arrays containing hundreds or thousands of oligonucleotidesprobes (Cronin et al. (1996) Human Mutation 7:244-255; Kozal et al.(1996) Nature Medicine 2:753-759). For example, genetic mutations can beidentified using two-dimensional arrays of light-generated DNA probesfixed to a surface, as described in Cronin et al., supra. Briefly, afirst hybridization array of probes can be used to scan through longstretches of DNA in a sample and control to identify base changesbetween the sequences by making linear arrays of sequential overlappingprobes. This step allows the identification of point mutations. Thisstep is followed by hybridization of the nucleic acid sample with asecond hybridization array in order to characterize specific mutationsusing smaller, specialized probe arrays complementary to many or allpotential variants or mutations. Each mutation array is composed ofparallel probe sets, one complementary to the wild-type gene and theother complementary to the mutant gene.

[1042] In yet another embodiment, any of a variety of sequencing methodsknown in the art can be used to directly sequence the selected gene anddetect mutations by comparing the sequence of the sample nucleic acidswith the corresponding wild-type (control) sequence. Examples ofsequencing reactions include those based on techniques developed byMaxim and Gilbert ((1977) Proc. Natl. Acad. Sci. USA 74:560) or Sanger((1977) Proc. Natl. Acad. Sci. USA 74:5463). It is also contemplatedthat any of a variety of automated sequencing procedures can be usedwhen performing the diagnostic assays ((1995) Bio/Techniques 19:448),including sequencing by mass spectrometry (see, e.g., PCT PublicationNo. WO 94/16101; Cohen et al. (1996) Adv. Chromatogr. 36:127-162; andGriffin et al. (1993) Appl.

[1043] Biochem. Biotechnol. 38:147-159).

[1044] Other methods for detecting mutations in a selected gene includemethods in which protection from cleavage agents is used to detectmismatched bases in RNA/RNA or RNA/DNA heteroduplexes (Myers et al.(1985) Science 230:1242). In general, the technique of mismatch cleavageentails providing heteroduplexes formed by hybridizing (labeled) RNA orDNA containing the wild-type sequence with potentially mutant RNA or DNAobtained from a tissue sample. The double-stranded duplexes are treatedwith an agent that cleaves single-stranded regions of the duplex such asthose which exist due to base pair mismatches between the control andsample strands. RNA/DNA duplexes can be treated with RNase to digestmismatched regions, and DNA/DNA hybrids can be treated with S1 nucleaseto digest mismatched regions.

[1045] In other embodiments, DNA/DNA or RNA/DNA duplexes can be treatedwith hydroxylamine or osmium tetroxide and with piperidine in order todigest mismatched regions. After digestion of the mismatched regions,the resulting material is separated by size on denaturing polyacrylamidegels to determine the site of the mutated or mismatched region. See,e.g., Cotton et al. (1988) Proc. Natl. Acad. Sci. USA 85:4397; Saleebaet al. (1992) Methods Enzymol. 217:286-295. In one embodiment, thecontrol DNA or RNA is labeled for detection.

[1046] In still another embodiment, the mismatch cleavage reactionemploys one or more proteins that recognize mismatched base pairs indouble-stranded DNA (so called DNA mismatch repair enzymes) in definedsystems for detecting and mapping point mutations in cDNAs obtained fromsamples of cells. For example, the mutY enzyme of E. coli cleavesfollowing A residues at G/A mismatches and the thymidine DNA glycosylasefrom HeLa cells cleaves following T residues at G/T mismatches (Hsu etal. (1994) Carcinogenesis 15:1657-1662). According to one embodiment, aprobe based on a selected sequence, e.g., a wild-type sequence, ishybridized with a cDNA or other DNA product obtained from a testcell(s). The duplex is treated with a DNA mismatch repair enzyme, andthe cleavage products, if any, are detected using an electrophoresisprotocol or another polynucleotide-separating method. See, e.g., U.S.Pat. No. 5,459,039.

[1047] In other embodiments, alterations in electrophoretic mobility areused to identify mutations in genes. For example, single strandconformation polymorphism (SSCP) analysis can be used to detectdifferences in electrophoretic mobility between mutant and wild typenucleic acids (Orita et al. (1989) Proc. Natl. Acad. Sci. USA 86:2766;see also Cotton (1993) Mutat. Res. 285:125-144; Hayashi (1992) Genet.Anal. Tech. Appl. 9:73-79). Single-stranded DNA fragments of sample andcontrol nucleic acids are denatured and allowed to re-nature. Thesecondary structure of single-stranded nucleic acids varies according totheir nucleotide sequence, and the resulting alteration inelectrophoretic mobility enables detection of even a single base change.The DNA fragments can be labeled or detected using labeled probes. Thesensitivity of the assay can be enhanced by using RNA (rather than DNA),because the secondary structure of RNA is more sensitive to sequencechanges. In one embodiment, the method uses heteroduplex analysis toseparate double stranded heteroduplex molecules on the basis of changesin electrophoretic mobility (Keen et al. (1991) Trends Genet. 7:5).

[1048] In yet another embodiment, the movement of mutant or wild-typefragments in polyacrylamide gels containing a gradient of denaturant isassayed using denaturing gradient gel electrophoresis (DGGE), asdescribed (Myers et al. (1985) Nature 313:495). When DGGE is used as themethod of analysis, DNA is modified to ensure that it does notcompletely denature, for example by adding a ‘GC clamp’ of approximately40 nucleotide residues of high-melting GC-rich DNA to one or both endsof the DNA strands, for example using a PCR method. In a furtherembodiment, a temperature gradient is used in place of a denaturinggradient to identify differences in the mobility of control and sampleDNA (Rosenbaum and Reissner (1987) Biophys. Chem. 265:12753).

[1049] Examples of other techniques for detecting point mutationsinclude, but are not limited to, selective oligonucleotidehybridization, selective amplification, and selective primer extension.For example, oligonucleotide primers can be prepared in which the knownmutation is located centrally. The primers are hybridized with targetDNA under conditions which permit hybridization only if a perfectcomplementary nucleotide sequence match occurs (Saiki et al. (1986)Nature 324:163); Saiki et al. (1989) Proc. Natl. Acad. Sci. USA86:6230). Such allele specific oligonucleotides are hybridized withPCR-amplified target DNA or attached to a surface for hybridization.

[1050] Alternatively, allele specific amplification technology can beused in conjunction with the methods of the invention. Oligonucleotidesused as primers for specific amplification have a sequence complementaryto the nucleotide sequence of a mutation of interest in the center ofthe molecule, so that occurrence of amplification depends on occurrenceof the mutation in the sample nucleic acid (Gibbs et al. (1989) NucleicAcids Res. 17:2437-2448) or at the extreme 3′ end of one primer where,under appropriate conditions, mismatching can prevent or inhibitpolymerase extension (Prossner (1993) Tibtech 11:238). In addition, itcan be desirable to introduce a novel restriction site in the region ofthe mutation in order to facilitate cleavage-based detection (Gaspariniet al. (1992) Mol. Cell Probes 6:1). Amplification can be performedusing Taq ligase (Barany (1991) Proc. Natl. Acad. Sci. USA 88:189). Insuch cases, ligation will occur only if there is a perfect match at the3′ end of the 5′ sequence, thereby making it possible to assess thepresence of a known mutation at a specific site by looking for thepresence or absence of amplification.

[1051] The methods described herein can be performed, for example, usingpre-packaged diagnostic kits comprising at least one probe nucleic acidor antibody reagent described herein. Such kits can be used, forexample, in clinical settings to diagnose patients exhibiting symptomsor a family history of a disorder involving a gene encoding apolypeptide of the invention. Furthermore, any cell type or tissue inwhich the polypeptide of the invention is expressed (e.g., a bloodsample containing peripheral blood leukocytes for proteins which aresecreted or which occur on or in peripheral blood leukocytes) can beused in the prognostic assays described herein.

[1052] 3. Pharmacogenomics

[1053] Agents which have a stimulatory or inhibitory effect on activityor expression of a polypeptide of the invention, as identified by ascreening assay described herein for example, can be administered toindividuals to treat (prophylactically or therapeutically) disordersassociated with aberrant activity of the polypeptide. In conjunctionwith such treatment, the pharmacogenomics (i.e., the study of therelationship between an individual's genotype and that individual'sresponse to a foreign compound or drug) of the individual can beconsidered. Differences in metabolism of therapeutics can lead to severetoxicity or therapeutic failure by altering the relation between doseand blood concentration of the pharmacologically active drug. Thus, thepharmacogenomics of the individual permits selection of effective agents(e.g., drugs) for prophylactic or therapeutic treatments based on aconsideration of the individual's genotype. Such pharmacogenomics canfurther be used to determine appropriate dosages and therapeuticregimens. Accordingly, the activity of a polypeptide of the invention,expression of a nucleic acid of the invention, or mutation content of agene of the invention in an individual can be determined to facilitateselection of one or more appropriate agents for therapeutic orprophylactic treatment of the individual.

[1054] Pharmacogenomics deals with clinically significant hereditaryvariations in the response to drugs due to altered drug disposition andabnormal action in affected persons. See, e.g., Linder (1997) Clin.Chem. 43(2):254-266. In general, two types of pharmacogenetic conditionscan be differentiated. Genetic conditions transmitted as a single factoraltering the way drugs act on the body are referred to as “altered drugaction.” Genetic conditions transmitted as single factors altering theway the body acts on drugs are referred to as “altered drug metabolism”.These pharmacogenetic conditions can occur either as rare defects or aspolymorphisms. For example, glucose-6-phosphate dehydrogenase (G6PD)deficiency is a common inherited enzymopathy in which the main clinicalcomplication is hemolysis after ingestion of oxidant drugs(anti-malarials, sulfonamides, analgesics, nitrofurans) and consumptionof fava beans.

[1055] As an illustrative embodiment, the activity of drug metabolizingenzymes is a major determinant of both the intensity and duration ofdrug action. The discovery of genetic polymorphisms of drug metabolizingenzymes (e.g., N-acetyltransferase 2 {NAT 2} and cytochrome P450 enzymesCYP2D6 and CYP2C19) explains why some patients do not obtain theexpected drug effects or exhibit exaggerated drug response and serioustoxicity following administration of standard and safe doses of a drug.These polymorphisms are expressed in two phenotypes in the population,the extensive metabolizer (EM) and poor metabolizer (PM). The prevalenceof PM is different among different populations. For example, the geneencoding CYP2D6 is highly polymorphic, and several mutations have beenidentified in PM. Each of these mutations results in absence offunctional CYP2D6. Poor metabolizers of CYP2D6 and CYP2C19 frequentlyexperience exaggerated drug response and side effects when they receivestandard doses. If a metabolite is the active therapeutic moiety, a PMwill show no therapeutic response, as demonstrated for the analgesiceffect of codeine mediated by its CYP2D6-formed metabolite morphine. Atthe other extreme are the so called ultra-rapid metabolizers who do notrespond to standard doses. Recently, the molecular basis of ultra-rapidmetabolism has been identified to be due to CYP2D6 gene amplification.

[1056] Thus, activity of a polypeptide of the invention, expression of anucleic acid encoding the polypeptide, or mutation content of a geneencoding the polypeptide in an individual can be determined tofacilitate selection of appropriate agents for therapeutic orprophylactic treatment of the individual. In addition, pharmacogeneticstudies can be used to apply genotyping of polymorphic alleles encodingdrug-metabolizing enzymes to identification of an individual's drugresponsiveness phenotype. This knowledge, when applied to dosing or drugselection, can avoid adverse reactions or therapeutic failure and thusenhance therapeutic or prophylactic efficiency when treating a subjectwith a modulator of activity or expression of the polypeptide, such as amodulator identified by one of the examples of screening assaysdescribed herein.

[1057] 4. Monitoring of Effects During Clinical Trials

[1058] Monitoring the influence of agents (e.g., drug compounds) onexpression or activity of a polypeptide of the invention (e.g., abilityto modulate aberrant cell proliferation chemotaxis, differentiation, orboth) can be applied not only in basic drug screening, but also inclinical trials. For example, the effectiveness of an agent, asdetermined by a screening assay as described herein, to increase geneexpression, protein levels, or protein activity can be monitored inclinical trials of subjects exhibiting decreased gene expression,protein levels, or protein activity. Alternatively, the effectiveness ofan agent, as determined by a screening assay, to decrease geneexpression, protein levels, or protein activity can be monitored inclinical trials of subjects exhibiting increased gene expression,protein levels, or protein activity. In such clinical trials, expressionor activity of a polypeptide of the invention and, optionally, that ofother polypeptide that have been implicated in similar disorders, can beused as a marker of the immune responsiveness of a particular cell.

[1059] For example, genes (including those of the invention) that aremodulated in cells by treatment with an agent (e.g., a peptide, a drug,or another small molecule) which modulates activity or expression of apolypeptide of the invention (e.g., as identified in a screening assaydescribed herein) can be identified. Thus, to study the effect of agentson cellular proliferation disorders, for example, in a clinical trial,cells can be isolated and their RNA can be prepared and analyzed todetermine the level of expression of one or more genes of the inventionand, optionally, other genes implicated in the disorder. The levels ofgene expression (i.e., a gene expression pattern) can be quantified byNorthern blot analysis or by RT-PCR, as described herein, or byassessing the amount of protein produced, by one of the methods asdescribed herein, or by measuring the level of activity of a gene of theinvention or other gene(s). In this way, the gene expression pattern canserve as an indicator of the physiological response of the cells to theagent. Accordingly, this response state can be determined before, and atvarious points during, or after treatment of the individual with theagent (or, of course, at more than one of these stages).

[1060] In one embodiment, the present invention provides a method formonitoring the effectiveness of treatment of a subject with an agent(e.g., an agonist, antagonist, peptidomimetic, protein, peptide, nucleicacid, small molecule, or other drug candidate identified by thescreening assays described herein) comprising (i) obtaining apre-administration sample from a subject prior to administration of theagent; (ii) detecting the level of the polypeptide or nucleic acid ofthe invention in the pre-administration sample; (iii) obtaining one ormore post-administration samples from the subject; (iv) detecting thelevel the of the polypeptide or nucleic acid of the invention in thepost-administration sample(s); (v) comparing the level of thepolypeptide or nucleic acid of the invention in the pre-administrationsample with the level of the polypeptide or nucleic acid of theinvention in the post-administration sample(s); and (vi) altering theadministration of the agent to the subject accordingly. For example,increased administration of the agent can be desirable to increase theexpression or activity of the polypeptide to levels higher than thosedetected, i.e., to increase the effectiveness of the agent.Alternatively, decreased administration of the agent can be desirable todecrease expression or activity of the polypeptide to levels lower thanthose detected, i.e., to decrease the effectiveness of the agent.

[1061] C. Methods of Treatment

[1062] The present invention provides both prophylactic and therapeuticmethods of treating a subject afflicted with, at risk for developing, orsusceptible to a disorder associated with aberrant expression oractivity of a polypeptide of the invention. Such disorders are describedelsewhere in this disclosure.

[1063] 1. Prophylactic Methods

[1064] In one aspect, the invention provides a method for preventing ina subject, a disorder associated with aberrant expression or activity ofa polypeptide of the invention, by administering to the subject an agentwhich modulates expression of the polypeptide or at least one activityof the polypeptide. Subjects at risk for a disease which is caused orcontributed to by aberrant expression or activity of a polypeptide ofthe invention can be identified by, for example, any one or combinationof the diagnostic and prognostic assays described herein. Administrationof a prophylactic agent can occur prior to the manifestation of symptomscharacteristic of the aberrance, so that the disease or disorder isprevented or, alternatively, delayed in its onset or progression.Depending on the type of aberrance, for example, an agonist orantagonist agent can be used for treating the subject. The appropriateagent can be determined based on screening assays described herein.

[1065] 2. Therapeutic Methods

[1066] Another aspect of the invention pertains to methods of modulatingexpression or activity of a polypeptide of the invention for therapeuticpurposes. The modulatory method of the invention involves contacting acell with an agent that modulates one or more of the activities of thepolypeptide. An agent that modulates activity can be an agent asdescribed herein, such as a nucleic acid, or a protein, anaturally-occurring cognate ligand of the polypeptide, a peptide, apeptidomimetic, or a small molecule. In one embodiment, the agentstimulates one or more of the biological activities of the polypeptide.Examples of such stimulatory agents include a polypeptide of theinvention, a biologically active portion of such a polypeptide, aportion of such a polypeptide which comprises an epitope of the nativepolypeptide, and a nucleic acid molecule encoding the polypeptide of theinvention that has been introduced into the cell. In another embodiment,the agent inhibits a biological activity of the polypeptide of theinvention or expression of a protein or nucleic acid of the invention.Examples of such inhibitory agents include antisense nucleic acidmolecules and antibodies. These modulatory methods can be performed invitro (e.g., by culturing the cell with the agent) or, alternatively, invivo (e.g., by administering the agent to a subject). As such, thepresent invention provides methods of treating an individual afflictedwith a disease or disorder characterized by aberrant expression oractivity of a polypeptide of the invention. In one embodiment, themethod involves administering an agent (e.g., an agent identified by ascreening assay described herein), or combination of agents thatmodulates (e.g., up-regulates or down-regulates) expression or activity.In another embodiment, the method involves administering a polypeptideof the invention or a nucleic acid molecule of the invention as therapyto compensate or substitute for reduced or aberrant expression oractivity of the polypeptide.

[1067] Stimulation of activity is desirable in situations in whichactivity or expression is abnormally low or in which increased activityis likely to have a beneficial effect. Conversely, inhibition ofactivity is desirable in situations in which activity or expression isabnormally high or in which decreased activity is likely to have abeneficial effect.

[1068] The contents of all references, patents, and published patentapplications cited in this disclosure are hereby incorporated byreference.

[1069] Deposits of Clones

[1070] Clones containing one or more cDNA molecules encodingpolypeptides of the invention have been deposited with the American TypeCulture Collection (ATCC®; 10801 University Boulevard, Manassas, Va.20110-2209) on dates disclosed herein, and these deposits were assignedthe Accession Numbers disclosed herein. These deposits will bemaintained under the terms of the Budapest Treaty on the InternationalRecognition of the Deposit of Microorganisms for the Purposes of PatentProcedure. These deposits were made merely as a convenience for those ofskill in the art and are not an admission that any deposit is requiredin order to comply with 35 U.S.C. §112.

[1071] Where a clone containing multiple cDNA molecules was deposited,the following standard digest procedure can be used to liberatefragments corresponding to individual cDNA molecules, except asotherwise described. To isolate the cDNA clone, an aliquot of thedeposited clone can be streaked out to yield single colonies on nutrientmedium (e.g., Luria broth plates) supplemented with 100 micrograms permilliliter ampicillin. Single colonies are grown, and plasmid DNA isextracted from single colonies using a standard mini-preparationprocedure. Next, a sample of the DNA mini-preparation is digested usinga combination of the restriction enzymes Sal I and Not I, and theresulting products are resolved on a 0.8% (w/v) agarose gel usingstandard DNA electrophoresis conditions.

[1072] A clone containing a cDNA molecule encoding TANGO 416 (cloneEpT416), was deposited with the American Type Culture Collection (ATCC®;10801 University Boulevard, Manassas, Va. 20110-2209) on Apr. 26, 1999as Accession Number PTA-1764, as an Escherichia coli strain carrying arecombinant plasmid harboring the clone. The standard digest procedureliberates a fragment as follows:

[1073] TANGO 416 (EpT416): 5.1 kilobases.

[1074] The identity of the strain containing TANGO 416 can be inferredfrom the liberation of a fragment of the above identified size.

[1075] A clone containing a cDNA molecule encoding TANGO 457 (clone457), was deposited with the ATCC® on Oct. 1, 1999 as Accession NumberPTA-817, as part of a composite deposit representing a mixture of fourstrains, each carrying one recombinant plasmid harboring a particularcDNA clone. The standard digest procedure liberates a fragment asfollows:

[1076] TANGO 457 (457): 2.3 kilobases

[1077] The identity of the strain containing TANGO 457 can be inferredfrom the liberation of a fragment of the above identified size.

[1078] Clones containing cDNA molecules encoding TANGO 229 and INTERCEPT289 (clones EpT229 and EpI289, respectively), were deposited with theATCC® on Oct. 1, 1999 as Accession No. PTA-295, as part of a compositedeposit representing a mixture of four strains, each carrying onerecombinant plasmid harboring a particular cDNA clone. The standarddigest procedure liberates fragments as follows:

[1079] TANGO 229 (EpT229): 3.6 kilobases

[1080] INTERCEPT 289 (Ep1289): 1.9 kilobases

[1081] The identity of the strains can be inferred from the fragmentsliberated.

[1082] Clones containing cDNA molecules encoding INTERCEPT 429 (cloneEpI429), were deposited with the ATCC® on Aug. 5, 1999 as Accession No.PTA-455, as part of a composite deposit representing a mixture of threestrains, each carrying one recombinant plasmid harboring a particularcDNA clone. The standard digest procedure liberates a fragment asfollows:

[1083] INTERCEPT 429 (EpI429): 0.5 kilobase

[1084] The identity of the strain containing INTERCEPT 429 can beinferred from the liberation of a fragment of the above identified size.

[1085] Clones containing cDNA molecules encoding INTERCEPT 309 and MANGO419 (clones EpT309 and EpT419, respectively), were deposited with theATCC® on Jan. 6, 2000 as Accession Number PTA-1156, as part of acomposite deposit representing a mixture of four strains, each carryingone recombinant plasmid harboring a particular cDNA clone. The standarddigest procedure liberates fragments as follows:

[1086] TANGO 309 (EpT309): 1.9 kilobases

[1087] MANGO 419 (EpT419): 0.3 kilobases

[1088] The identity of the strains can be inferred from the fragmentsliberated.

[1089] Clones containing cDNA molecules encoding TANGO 366 and INTERCEPT394 (clones Aped and 394, respectively), were deposited with the ATCC®on Jul. 23, 1999 as Accession No. PTA-424, as part of a compositedeposit representing a mixture of five strains, each carrying onerecombinant plasmid harboring a particular cDNA clone. The standarddigest procedure liberates fragments as follows:

[1090] TANGO 366 (EpT366): 2.6 kilobase pairs

[1091] INTERCEPT 394 (394): 3.7 kilobase pairs

[1092] The identity of the strains can be inferred from the fragmentsliberated.

[1093] Clones containing cDNA molecules encoding TANGO 210 and INTERCEPT400 (clones Aped and 400, respectively), were deposited with the ATCC®on Jul. 29, 1999 as Accession No. PTA-438, as part of a compositedeposit representing a mixture of five strains, each carrying onerecombinant plasmid harboring a particular cDNA clone. The standarddigest procedure liberates fragments as follows:

[1094] TANGO 210 (EpT210): 1.7 kilobase pairs

[1095] INTERCEPT 400 (400): 3.0 kilobase pairs

[1096] The identity of the strains can be inferred from the fragmentsliberated.

[1097] Clones comprising cDNA molecules encoding human INTERCEPT 217,human INTERCEPT 297, and human TANGO 331 were deposited with ATCC® onMay 28, 1999, as part of a composite deposit representing a mixture offive strains, each carrying one recombinant plasmid harboring aparticular cDNA clone. This deposit was assigned Accession NumberPTA-147. The standard digest procedure (except that restriction enzymesSalI, NotI, and SmaI are used) liberates fragments as follows:

[1098] 1. human INTERCEPT 217 (clone EpT217): 2.9 kilobases

[1099] 2. human INTERCEPT 297 (clone EpT297): 1.2 kilobases and 0.3kilobases (human INTERCEPT 297 has a SmaI cut site at about base pair1183).

[1100] 3. human TANGO 331 (clone EpT331): 1.4 kilobases

[1101] The identity of the strains can be inferred from the fragmentsliberated.

[1102] Human TANGO 276, human TANGO 292, human TANGO 332, human TANGO202, human TANGO 234, and human TANGO 265 were each deposited as singledeposits. Their clone names, deposit dates, and accession numbers are asfollows:

[1103] 1. human TANGO 276: clone EpT276 was deposited with ATCC® on May28, 1999, and was assigned Accession Number PTA-150.

[1104] 2. human TANGO 292: clone EpT292 was deposited with ATCC® on Apr.28, 1999, and was assigned Accession Number 207230.

[1105] 3. human TANGO 332: clone EpT332 was deposited with ATCC® on May28, 1999, and was assigned Accession Number PTA-151.

[1106] 4. human TANGO 202: clone EpT202 was deposited with ATCC® on Apr.21, 1999, and was assigned Accession Number 207219.

[1107] 5. human TANGO 234: clone EpT234 was deposited with ATCC® on Apr.2, 1999, and was assigned Accession Number 207184.

[1108] 6. human TANGO 265: clone EpT265 was deposited with ATCC® on Apr.28, 1999, and was assigned Accession Number 207228.

[1109] Clones containing cDNA molecules encoding human TANGO 286, humanTANGO 294, and INTERCEPT 296 were deposited with ATCC® on Apr. 21, 1999as Accession Number 207220, as part of a composite deposit representinga mixture of five strains, each carrying one recombinant plasmidharboring a particular cDNA clone. The standard digest procedure (exceptthat restriction enzymes SalI, NotI, and DraII are used) liberatesfragments as follows:

[1110] 1. human TANGO 286 (clone EpT286): 1.85 kilobases and 1 kilobases(human TANGO 286 has a DraII cut site at about base pair 1856).

[1111] 2. human TANGO 294 (clone EpT294): 1.4 kilobases and 0.6kilobases (human TANGO 294 has a DraII cut site at about base pair1447).

[1112] 3. human INTERCEPT 296 (clone EpT296): 0.4 kilobases, 1.6kilobases, and 0.1 kilobases (human INTERCEPT 296 has DraII cut sites atabout base pair 410 and at about base pair 1933).

[1113] The identity of the strains can be inferred from the fragmentsliberated.

[1114] A clone containing a cDNA molecule encoding mouse TANGO 202 wasdeposited with ATCC® on Apr. 21, 1999 and was assigned Accession Number207221, as part of a composite deposit representing a mixture of fivestrains, each carrying one recombinant plasmid harboring a particularcDNA clone. The standard digest procedure (except that restrictionenzymes SalI, NotI, and ApaI are used) liberates a fragment as follows:

[1115] mouse TANGO 202 (clone EpTm202): 3.5 kilobases and 1.4 kilobases(mouse

[1116] TANGO 202 has a Apa I cut site at about base pair 3519).

[1117] The identity of the strain can be inferred from the fragmentliberated.

[1118] Equivalents

[1119] Those skilled in the art will recognize, or be able to ascertainusing no more than routine experimentation, many equivalents to thespecific embodiments of the invention described herein. Such equivalentsare encompassed by the following claims.

0 SEQUENCE LISTING The patent application contains a lengthy “SequenceListing” section. A copy of the “Sequence Listing” is available inelectronic form from the USPTO web site(http://seqdata.uspto.gov/sequence.html?DocID=20040121396). Anelectronic copy of the “Sequence Listing” will also be available fromthe USPTO upon request and payment of the fee set forth in 37 CFR1.19(b)(3).

What is claimed is:
 1. An isolated nucleic acid molecule selected fromthe group consisting of: a) a nucleic acid molecule having a nucleotidesequence which is at least 90% identical to the nucleotide sequence ofany of SEQ ID NOs: 1, 2, 31, 32, 51, 52, 71, 72, 81, 82, 91, 92, 96, 97,101, 102, 106, 107, 111, 112, 121, 122, 141, 142, 151, 152, 161, 162,171, 172, 181, 182, 191, 192, 201, 202, 215, 217, 221, 222, 241, 242,251, 252, 271, 272, 279, 280, 303, 304, 308, 309, 324, 325, 329, 330,351, 352, 362, 371, 372, 379, 380, 387, 388, 403, 404, 415, 416, 423,424, 437, 438, and the nucleotide sequence of any of the clonesdeposited as ATCC® Accession numbers 207184, 207219, 207220, 207221,207228, 207230, PTA-147, PTA-150, PTA-151, PTA-295, PTA-424, PTA-438,PTA-455, PTA-817, PTA-1156, and PTA-1764, or a complement thereof; b) anucleic acid molecule comprising at least 15 nucleotide residues andhaving a nucleotide sequence identical to at least 15 consecutivenucleotide residues of any of SEQ ID NOs: 1, 2, 31, 32, 51, 52, 71, 72,81, 82, 91, 92, 96, 97, 101, 102, 106, 107, 111, 112, 121, 122, 141,142, 151, 152, 161, 162, 171, 172, 181, 182, 191, 192, 201, 202, 215,217, 221, 222, 241, 242, 251, 252, 271, 272, 279, 280, 303, 304, 308,309, 324, 325, 329, 330, 351, 352, 362, 371, 372, 379, 380, 387, 388,403, 404, 415, 416, 423, 424, 437, 438, and the nucleotide sequence ofany of the clones deposited as ATCC® Accession numbers 207184, 207219,207220, 207221, 207228, 207230, PTA-147, PTA-150, PTA-151, PTA-295,PTA-424, PTA-438, PTA-455, PTA-817, PTA-1156, and PTA-1764, or acomplement thereof, c) a nucleic acid molecule which encodes apolypeptide comprising the amino acid sequence of any of SEQ ID NOs:3-8, 33, 35, 38, 53-60, 73-78, 83-85, 93-95, 98-100, 103-105, 108-110,113-115, 123-131, 143-145, 153-160, 163, 173-175, 183-185, 193-198,203-214, 216, 223-236, 243-252, 253, 273-278, 281-302, 305-307, 310-315,326-328, 331-333, 353-358, 363-368, 373-378, 381-386, 389-394, 405-414,417-422, 425-436, and 439, and the amino acid sequence encoded by thenucleotide sequence of any of the clones deposited as ATCC® Accessionnumbers 207184, 207219, 207220, 207221, 207228, 207230, PTA-147,PTA-150, PTA-151, PTA-295, PTA-424, PTA-438, PTA-455, PTA-817, PTA-1156,and PTA-1764; d) a nucleic acid molecule which encodes a fragment of apolypeptide comprising the amino acid sequence of any of SEQ ID NOs:3-8, 33, 35, 38, 53-60, 73-78, 83-85, 93-95, 98-100, 103-105, 108-110,113-115, 123-131, 143-145, 153-160, 163, 173-175, 183-185, 193-198,203-214, 216, 223-236, 243-252, 253, 273-278, 281-302, 305-307, 310-315,326-328, 331-333, 353-358, 363-368, 373-378, 381-386, 389-394, 405-414,417-422, 425-436, and 439 and the amino acid sequence encoded by thenucleotide sequence of any of the clones deposited as ATCC® Accessionnumbers 207184, 207219, 207220, 207221, 207228, 207230, PTA-147,PTA-150, PTA-151, PTA-295, PTA-424, PTA-438, PTA-455, PTA-817, PTA-1156,and PTA-1764, wherein the fragment comprises at least 10 consecutiveamino acid residues of any of SEQ ID NOs: 3-8, 33, 35, 38, 53-60, 73-78,83-85, 93-95, 98-100, 103-105, 108-110, 113-115, 123-131, 143-145,153-160, 163, 173-175, 183-185, 193-198, 203-214, 216, 223-236, 243-252,253, 273-278, 281-302, 305-307, 310-315, 326-328, 331-333, 353-358,363-368, 373-378, 381-386, 389-394, 405-414, 417-422, 425-436, and 439and the amino acid sequence encoded by the nucleotide sequence of any ofthe clones deposited as ATCC® Accession numbers 207184, 207219, 207220,207221, 207228, 207230, PTA-147, PTA-150, PTA-151, PTA-295, PTA-424,PTA-438, PTA-455, PTA-817, PTA-1156, and PTA-1764; and e) a nucleic acidmolecule which encodes a fragment of a polypeptide comprising the aminoacid sequence of any of SEQ ID NOs: 3, 53, 73, 83, 93, 98, 103, 108,113, 123, 143, 153, 163, 173, 183, 193, 203, 223, 243, 253, 273, 281,305, 310, 326, 331, 353, 363, 373, 381, 389, 405, 417, 425, and 439 andthe amino acid sequence encoded by the nucleotide sequence of any of theclones deposited as ATCC® Accession numbers 207184, 207219, 207220,207221, 207228, 207230, PTA-147, PTA-150, PTA-151, PTA-295, PTA-424,PTA-438, PTA-455, PTA-817, PTA-1156, and PTA-1764, wherein the fragmentcomprises consecutive amino acid residues corresponding to at least halfof the full length of any of SEQ ID NOs: 3, 53, 73, 83, 93, 98, 103,108, 113, 123, 143, 153, 163, 173, 183, 193, 203, 223, 243, 253, 273,281, 305, 310, 326, 331, 353, 363, 373, 381, 389, 405, 417, 425, and 439and the amino acid sequence encoded by the nucleotide sequence of any ofthe clones deposited as ATCC® Accession numbers 207184, 207219, 207220,207221, 207228, 207230, PTA-147, PTA-150, PTA-151, PTA-295, PTA-424,PTA-438, PTA-455, PTA-817, PTA-1156, and PTA-1764; and f) a nucleic acidmolecule which encodes a naturally occurring allelic variant of apolypeptide comprising the amino acid sequence of any of SEQ ID NOs:3-8, 33, 35, 38, 53-60, 73-78, 83-85, 93-95, 98-100, 103-105, 108-110,113-115, 123-131, 143-145, 153-160, 163, 173-175, 183-185, 193-198,203-214, 216, 223-236, 243-252, 253, 273-278, 281-302, 305-307, 310-315,326-328, 331-333, 353-358, 363-368, 373-378, 381-386, 389-394, 405-414,417-422, 425-436, and 439, wherein the nucleic acid molecule hybridizeswith a nucleic acid molecule consisting of the nucleotide sequence ofany of SEQ ID NOs: 1, 2, 31, 32, 51, 52, 71, 72, 81, 82, 91, 92, 96, 97,101, 102, 106, 107, 111, 112, 121, 122, 141, 142, 151, 152, 161, 162,171, 172, 181, 182, 191, 192, 201, 202, 215, 217, 221, 222, 241, 242,251, 252, 271, 272, 279, 280, 303, 304, 308, 309, 324, 325, 329, 330,351, 352, 362, 371, 372, 379, 380, 387, 388, 403, 404, 415, 416, 423,424, 437, 438, and the nucleotide sequence of any of the clonesdeposited as ATCC® Accession numbers 207184, 207219, 207220, 207221,207228, 207230, PTA-147, PTA-150, PTA-151, PTA-295, PTA-424, PTA-438,PTA-455, PTA-817, PTA-1156, and PTA-1764, or a complement thereof understringent conditions.
 2. The isolated nucleic acid molecule of claim 1,which is selected from the group consisting of: a) a nucleic acid havingthe nucleotide sequence of any of SEQ ID NOs: 1, 2, 31, 32, 51, 52, 71,72, 81, 82, 91, 92, 96, 97, 101, 102, 106, 107, 111, 112, 121, 122, 141,142, 151, 152, 161, 162, 171, 172, 181, 182, 191, 192, 201, 202, 215,217, 221, 222, 241, 242, 251, 252, 271, 272, 279, 280, 303, 304, 308,309, 324, 325, 329, 330, 351, 352, 362, 371, 372, 379, 380, 387, 388,403, 404, 415, 416, 423, 424, 437, 438, and the nucleotide sequence ofany of the clones deposited as ATCC® Accession numbers 207184, 207219,207220, 207221, 207228, 207230, PTA-147, PTA-150, PTA-151, PTA-295,PTA-424, PTA-438, PTA-455, PTA-817, PTA-1156, and PTA-1764, or acomplement thereof; and b) a nucleic acid molecule which encodes apolypeptide having the amino acid sequence of any of SEQ ID NOs: 3-8,33, 35, 38, 53-60, 73-78, 83-85, 93-95, 98-100, 103-105, 108-110,113-115, 123-131, 143-145, 153-160, 163, 173-175, 183-185, 193-198,203-214, 216, 223-236, 243-252, 253, 273-278, 281-302, 305-307, 310-315,326-328, 331-333, 353-358, 363-368, 373-378, 381-386, 389-394, 405-414,417-422, 425-436, and 439 and the amino acid sequence encoded by thenucleotide sequence of any of the clones deposited as ATCC® Accessionnumbers 207184, 207219, 207220, 207221, 207228, 207230, PTA-147,PTA-150, PTA-151, PTA-295, PTA-424, PTA-438, PTA-455, PTA-817, PTA-1156,and PTA-1764, or a complement thereof.
 3. The nucleic acid molecule ofclaim 1, further comprising vector nucleic acid sequences.
 4. Thenucleic acid molecule of claim 1 further comprising nucleic acidsequences encoding a heterologous polypeptide.
 5. A host cell whichcontains the nucleic acid molecule of claim
 1. 6. The host cell of claim5 which is a mammalian host cell.
 7. A non-human mammalian host cellcontaining the nucleic acid molecule of claim
 1. 8. An isolatedpolypeptide selected from the group consisting of: a) a fragment of apolypeptide comprising the amino acid sequence of any of SEQ ID NOs:3-8, 33, 35, 38, 53-60, 73-78, 83-85, 93-95, 98-100, 103-105, 108-110,113-115, 123-131, 143-145, 153-160, 163, 173-175, 183-185,193-198,203-214, 216, 223-236, 243-252, 253, 273-278, 281-302, 305-307,310-315, 326-328, 331-333, 353-358, 363-368, 373-378, 381-386, 389-394,405-414, 417-422, 425-436, and 439 and the amino acid sequence encodedby the nucleotide sequence of any of the clones deposited as ATCC®Accession numbers 207184, 207219, 207220, 207221, 207228, 207230,PTA-147, PTA-150, PTA-151, PTA-295, PTA-424, PTA-438, PTA-455, PTA-817,PTA-1156, and PTA-1764; b) a naturally occurring allelic variant of apolypeptide comprising the amino acid sequence of any of SEQ ID NOs:3-8, 33, 35, 38, 53-60, 73-78, 83-85, 93-95, 98-100, 103-105, 108-110,113-115, 123-131, 143-145, 153-160, 163, 173-175, 183-185, 193-198,203-214, 216, 223-236, 243-252, 253, 273-278, 281-302, 305-307, 310-315,326-328, 331-333, 353-358, 363-368, 373-378, 381-386, 389-394, 405-414,417-422, 425-436, and 439, wherein the polypeptide is encoded by anucleic acid molecule which hybridizes with a nucleic acid moleculeconsisting of the nucleotide sequence of any of SEQ ID NOs: 1, 2, 31,32, 51, 52, 71, 72, 81, 82, 91, 92, 96, 97, 101, 102, 106, 107, 111,112, 121, 122, 141, 142, 151, 152, 161, 162, 171, 172, 181, 182, 191,192, 201, 202, 215, 217, 221, 222, 241, 242, 251, 252, 271, 272, 279,280, 303, 304, 308, 309, 324, 325, 329, 330, 351, 352, 362, 371, 372,379, 380, 387, 388, 403, 404, 415, 416, 423, 424, 437, 438, and thenucleotide sequence of any of the clones deposited as ATCC® Accessionnumbers 207184, 207219, 207220, 207221, 207228, 207230, PTA-147,PTA-150, PTA-151, PTA-295, PTA-424, PTA-438, PTA-455, PTA-817, PTA-1156,and PTA-1764, or a complement thereof under stringent conditions; and c)a polypeptide which is encoded by a nucleic acid molecule comprising anucleotide sequence which is at least 90% identical to a nucleic acidconsisting of the nucleotide sequence of any of SEQ ID NOs: 1, 2, 31,32, 51, 52, 71, 72, 81, 82, 91, 92, 96, 97, 101, 102, 106, 107, 111,112, 121, 122, 141, 142, 151, 152, 161, 162, 171, 172, 181, 182, 191,192, 201, 202, 215, 217, 221, 222, 241, 242, 251, 252, 271, 272, 279,280, 303, 304, 308, 309, 324, 325, 329, 330, 351, 352, 362, 371, 372,379, 380, 387, 388, 403, 404, 415, 416, 423, 424, 437, 438, and thenucleotide sequence of any of the clones deposited as ATCC® Accessionnumbers 207184, 207219, 207220, 207221, 207228, 207230, PTA-147,PTA-150, PTA-151, PTA-295, PTA-424, PTA-438, PTA-455, PTA-817, PTA-1156,and PTA-1764, or a complement thereof.
 9. The isolated polypeptide ofclaim 8 having the amino acid sequence of any of SEQ ID NOs: 3-8, 33,35, 38, 53-60, 73-78, 83-85, 93-95, 98-100, 103-105, 108-110, 113-115,123-131, 143-145, 153-160, 163, 173-175, 183-185, 193-198, 203-214, 216,223-236, 243-252, 253, 273-278, 281-302, 305-307, 310-315, 326-328,331-333, 353-358, 363-368, 373-378, 381-386, 389-394, 405-414, 417-422,425-436, and 439 and the amino acid sequence encoded by the nucleotidesequence of any of the clones deposited as ATCC® Accession numbers207184, 207219, 207220, 207221, 207228, 207230, PTA-147, PTA-150,PTA-151, PTA-295, PTA-424, PTA-438, PTA-455, PTA-817, PTA-1156, andPTA-1764.
 10. The polypeptide of claim 8, wherein the amino acidsequence of the polypeptide further comprises heterologous amino acidresidues.
 11. An antibody which selectively binds with the polypeptideof claim
 8. 12. A method for producing a polypeptide selected from thegroup consisting of: a) a polypeptide comprising the amino acid sequenceof any of SEQ ID NOs: 3-8, 33, 35, 38, 53-60, 73-78, 83-85, 93-95,98-100, 103-105, 108-110, 113-115, 123-131, 143-145, 153-160, 163,173-175, 183-185, 193-198, 203-214, 216, 223-236, 243-252, 253, 273-278,281-302, 305-307, 310-315, 326-328, 331-333, 353-358, 363-368, 373-378,381-386, 389-394, 405-414, 417-422, 425-436, and 439 and the amino acidsequence encoded by the nucleotide sequence of any of the clonesdeposited as ATCC® Accession numbers 207184, 207219, 207220, 207221,207228, 207230, PTA-147, PTA-150, PTA-151, PTA-295, PTA-424, PTA-438,PTA-455, PTA-817, PTA-1156, and PTA-1764; b) a polypeptide comprising afragment of the amino acid sequence of any of SEQ ID NOs: 3-8, 33, 35,38, 53-60, 73-78, 83-85, 93-95, 98-100, 103-105, 108-110, 113-115,123-131, 143-145, 153-160, 163, 173-175, 183-185, 193-198,203-214, 216,223-236, 243-252, 253, 273-278, 281-302, 305-307, 310-315, 326-328,331-333, 353-358, 363-368, 373-378, 381-386, 389-394, 405-414, 417-422,425-436, and 439 and the amino acid sequence encoded by the nucleotidesequence of any of the clones deposited as ATCC® Accession numbers207184, 207219, 207220, 207221, 207228, 207230, PTA-147, PTA-150,PTA-151, PTA-295, PTA-424, PTA-438, PTA-455, PTA-817, PTA-1156, andPTA-1764, wherein the fragment comprises at least 10 contiguous aminoacids of any of SEQ ID NOs: 3-8, 33, 35, 38, 53-60, 73-78, 83-85, 93-95,98-100, 103-105, 108-110, 113-115, 123-131, 143-145, 153-160, 163,173-175, 183-185, 193-198, 203-214, 216, 223-236, 243-252, 253, 273-278,281-302, 305-307, 310-315, 326-328, 331-333, 353-358, 363-368, 373-378,381-386, 389-394, 405-414, 417-422, 425-436, and 439 and the amino acidsequence encoded by the nucleotide sequence of any of the clonesdeposited as ATCC® Accession numbers 207184, 207219, 207220, 207221,207228, 207230, PTA-147, PTA-150, PTA-151, PTA-295, PTA-424, PTA-438,PTA-455, PTA-817, PTA-1156, and PTA-1764; and c) a naturally occurringallelic variant of a polypeptide comprising the amino acid sequence ofany of SEQ ID NOs: 3-8, 33, 35, 38, 53-60, 73-78, 83-85, 93-95, 98-100,103-105, 108-110, 113-115, 123-131, 143-145, 153-160, 163, 173-175,183-185, 193-198, 203-214, 216, 223-236, 243-252, 253, 273-278, 281-302,305-307, 310-315, 326-328, 331-333, 353-358, 363-368, 373-378, 381-386,389-394, 405-414, 417-422, 425-436, and 439, or a complement thereof,wherein the polypeptide is encoded by a nucleic acid molecule whichhybridizes with a nucleic acid molecule consisting of the nucleotidesequence of any of SEQ ID NOs: 1, 2, 31, 32, 51, 52, 71, 72, 81, 82, 91,92, 96, 97, 101, 102, 106, 107, 111, 112, 121, 122, 141, 142, 151, 152,161, 162, 171, 172, 181, 182, 191, 192, 201, 202, 215, 217, 221, 222,241, 242, 251, 252, 271, 272, 279, 280, 303, 304, 308, 309, 324, 325,329, 330, 351, 352, 362, 371, 372, 379, 380, 387, 388, 403, 404, 415,416, 423, 424, 437, 438, and the nucleotide sequence of any of theclones deposited as ATCC® Accession numbers 207184, 207219, 207220,207221, 207228, 207230, PTA-147, PTA-150, PTA-151, PTA-295, PTA-424,PTA-438, PTA-455, PTA-817, PTA-1156, and PTA-1764, or a complementthereof under stringent conditions; the method comprising culturing thehost cell of claim 5 under conditions in which the nucleic acid moleculeis expressed.
 13. A method for detecting the presence of a polypeptideof claim 8 in a sample, comprising: a) contacting the sample with acompound which selectively binds with a polypeptide of claim 8; and b)determining whether the compound binds with the polypeptide in thesample.
 14. The method of claim 13, wherein the compound which bindswith the polypeptide is an antibody.
 15. A kit comprising a compoundwhich selectively binds with a polypeptide of claim 8 and instructionsfor use.
 16. A method for detecting the presence of a nucleic acidmolecule of claim 1 in a sample, comprising the steps of: a) contactingthe sample with a nucleic acid probe or primer which selectivelyhybridizes with the nucleic acid molecule; and b) determining whetherthe nucleic acid probe or primer binds with a nucleic acid molecule inthe sample.
 17. The method of claim 16, wherein the sample comprisesmRNA molecules and is contacted with a nucleic acid probe.
 18. A kitcomprising a compound which selectively hybridizes with a nucleic acidmolecule of claim 1 and instructions for use.
 19. A method foridentifying a compound which binds with a polypeptide of claim 8comprising the steps of: a) contacting a polypeptide, or a cellexpressing a polypeptide of claim 8 with a test compound; and b)determining whether the polypeptide binds with the test compound. 20.The method of claim 19, wherein the binding of the test compound to thepolypeptide is detected by a method selected from the group consistingof: a) detection of binding by direct detecting of testcompound/polypeptide binding; b) detection of binding using acompetition binding assay; c) detection of binding using an assay for anactivity characteristic of the polypeptide.
 21. A method for modulatingthe activity of a polypeptide of claim 8 comprising contacting apolypeptide or a cell expressing a polypeptide of claim 8 with acompound which binds with the polypeptide in a sufficient concentrationto modulate the activity of the polypeptide.
 22. A method foridentifying a compound which modulates the activity of a polypeptide ofclaim 8, comprising: a) contacting a polypeptide of claim 8 with a testcompound; and b) determining the effect of the test compound on theactivity of the polypeptide to thereby identify a compound whichmodulates the activity of the polypeptide.
 23. An antibody substancewhich selectively binds with the polypeptide of claim
 8. 24. A method ofmaking an antibody substance which selectively binds with thepolypeptide of claim 8, the method comprising providing the polypeptideto an immunocompetent vertebrate and thereafter harvesting from thevertebrate blood or serum comprising the antibody substance.
 25. Amethod of making an antibody substance which selectively binds with thepolypeptide of claim 8, the method comprising contacting the polypeptidewith a plurality of particles which individually comprise an antibodysubstance and a nucleic acid encoding the antibody substance,segregating a particle which selectively binds with the polypeptide, andexpressing the antibody substance from the nucleic acid of thesegregated particle.
 26. The isolated nucleic acid of claim 1, whereinthe isolated nucleic acid comprises a portion having the nucleotidesequence SEQ ID NO:
 2. 27. The isolated nucleic acid of claim 1, whereinthe isolated nucleic acid comprises a portion having the nucleotidesequence SEQ ID NO:
 52. 28. The isolated nucleic acid of claim 1,wherein the isolated nucleic acid comprises a portion having thenucleotide sequence SEQ ID NO:
 72. 29. The isolated nucleic acid ofclaim 1, wherein the isolated nucleic acid comprises a portion havingthe nucleotide sequence of one of SEQ ID NOs: 82, 92, 97, 102, 107, and112.
 30. The isolated nucleic acid of claim 1, wherein the isolatednucleic acid comprises a portion having the nucleotide sequence SEQ IDNO:
 122. 31. The isolated nucleic acid of claim 1, wherein the isolatednucleic acid comprises a portion having the nucleotide sequence SEQ IDNO:
 142. 32. The isolated nucleic acid of claim 1, wherein the isolatednucleic acid comprises a portion having the nucleotide sequence SEQ IDNO:
 152. 33. The isolated nucleic acid of claim 1, wherein the isolatednucleic acid comprises a portion having the nucleotide sequence SEQ IDNO:
 172. 34. The isolated nucleic acid of claim 1, wherein the isolatednucleic acid comprises a portion having the nucleotide sequence SEQ IDNO:
 192. 35. The isolated nucleic acid of claim 1, wherein the isolatednucleic acid comprises a portion having the nucleotide sequence SEQ IDNO:
 202. 36. The isolated nucleic acid of claim 1, wherein the isolatednucleic acid comprises a portion having the nucleotide sequence SEQ IDNO:
 222. 37. The isolated nucleic acid of claim 1, wherein the isolatednucleic acid comprises a portion having the nucleotide sequence SEQ IDNO:
 272. 38. The isolated nucleic acid of claim 1, wherein the isolatednucleic acid comprises a portion having the nucleotide sequence SEQ IDNO:
 280. 39. The isolated nucleic acid of claim 1, wherein the isolatednucleic acid comprises a portion having the nucleotide sequence SEQ IDNO:
 304. 40. The isolated nucleic acid of claim 1, wherein the isolatednucleic acid comprises a portion having the nucleotide sequence SEQ IDNO:
 309. 41. The isolated nucleic acid of claim 1, wherein the isolatednucleic acid comprises a portion having the nucleotide sequence SEQ IDNO:
 325. 42. The isolated nucleic acid of claim 1, wherein the isolatednucleic acid comprises a portion having the nucleotide sequence SEQ IDNO:
 330. 43. The isolated nucleic acid of claim 1, wherein the isolatednucleic acid comprises a portion having the nucleotide sequence SEQ IDNO:
 372. 44. The isolated nucleic acid of claim 1, wherein the isolatednucleic acid comprises a portion having the nucleotide sequence SEQ IDNO:
 380. 45. The isolated nucleic acid of claim 1, wherein the isolatednucleic acid comprises a portion having the nucleotide sequence SEQ IDNO:
 388. 46. The isolated nucleic acid of claim 1, wherein the isolatednucleic acid comprises a portion having the nucleotide sequence SEQ IDNO:
 404. 47. The isolated nucleic acid of claim 1, wherein the isolatednucleic acid comprises a portion having the nucleotide sequence SEQ IDNO:
 416. 48. The isolated nucleic acid of claim 1, wherein the isolatednucleic acid comprises a portion having the nucleotide sequence SEQ IDNO:
 424. 49. The isolated nucleic acid of claim 1, wherein the isolatednucleic acid comprises a portion having the nucleotide sequence SEQ IDNO:
 162. 50. The isolated nucleic acid of claim 1, wherein the isolatednucleic acid comprises a portion having the nucleotide sequence SEQ IDNO:
 182. 51. The isolated nucleic acid of claim 1, wherein the isolatednucleic acid comprises a portion having the nucleotide sequence SEQ IDNO:
 242. 52. The isolated nucleic acid of claim 1, wherein the isolatednucleic acid comprises a portion having the nucleotide sequence SEQ IDNO:
 252. 53. The isolated nucleic acid of claim 1, wherein the isolatednucleic acid comprises a portion having the nucleotide sequence SEQ IDNO:
 362. 54. The isolated nucleic acid of claim 1, wherein the isolatednucleic acid comprises a portion having the nucleotide sequence SEQ IDNO:
 352. 55. The isolated nucleic acid of claim 1, wherein the isolatednucleic acid comprises a portion having the nucleotide sequence SEQ IDNO:
 438. 56. The isolated polypeptide of claim 8, wherein the amino acidsequence of the isolated polypeptide is SEQ ID NO:
 3. 57. The isolatedpolypeptide of claim 8, wherein the amino acid sequence of the isolatedpolypeptide is SEQ ID NO:
 53. 58. The isolated polypeptide of claim 8,wherein the amino acid sequence of the isolated polypeptide is SEQ IDNO:
 73. 59. The isolated polypeptide of claim 8, wherein the amino acidsequence of the isolated polypeptide is one of SEQ ID NOs: 83, 93, 98,103, 108, and
 113. 60. The isolated polypeptide of claim 8, wherein theamino acid sequence of the isolated polypeptide is SEQ ID NO:
 123. 61.The isolated polypeptide of claim 8, wherein the amino acid sequence ofthe isolated polypeptide is SEQ ID NO:
 143. 62. The isolated polypeptideof claim 8, wherein the amino acid sequence of the isolated polypeptideis SEQ ID NO:
 153. 63. The isolated polypeptide of claim 8, wherein theamino acid sequence of the isolated polypeptide is SEQ ID NO:
 173. 64.The isolated polypeptide of claim 8, wherein the amino acid sequence ofthe isolated polypeptide is SEQ ID NO:
 193. 65. The isolated polypeptideof claim 8, wherein the amino acid sequence of the isolated polypeptideis SEQ ID NO:
 203. 66. The isolated polypeptide of claim 8, wherein theamino acid sequence of the isolated polypeptide is SEQ ID NO:
 223. 67.The isolated polypeptide of claim 8, wherein the amino acid sequence ofthe isolated polypeptide is SEQ ID NO:
 273. 68. The isolated polypeptideof claim 8, wherein the amino acid sequence of the isolated polypeptideis SEQ ID NO:
 281. 69. The isolated polypeptide of claim 8, wherein theamino acid sequence of the isolated polypeptide is SEQ ID NO:
 305. 70.The isolated polypeptide of claim 8, wherein the amino acid sequence ofthe isolated polypeptide is SEQ ID NO:
 310. 71. The isolated polypeptideof claim 8, wherein the amino acid sequence of the isolated polypeptideis SEQ ID NO:
 326. 72. The isolated polypeptide of claim 8, wherein theamino acid sequence of the isolated polypeptide is SEQ ID NO:
 331. 73.The isolated polypeptide of claim 8, wherein the amino acid sequence ofthe isolated polypeptide is SEQ ID NO:
 373. 74. The isolated polypeptideof claim 8, wherein the amino acid sequence of the isolated polypeptideis SEQ ID NO:
 381. 75. The isolated polypeptide of claim 8, wherein theamino acid sequence of the isolated polypeptide is SEQ ID NO:
 389. 76.The isolated polypeptide of claim 8, wherein the amino acid sequence ofthe isolated polypeptide is SEQ ID NO:
 405. 77. The isolated polypeptideof claim 8, wherein the amino acid sequence of the isolated polypeptideis SEQ ID NO:
 417. 78. The isolated polypeptide of claim 8, wherein theamino acid sequence of the isolated polypeptide is SEQ ID NO:
 425. 79.The isolated polypeptide of claim 8, wherein the amino acid sequence ofthe isolated polypeptide is SEQ ID NO:
 163. 80. The isolated polypeptideof claim 8, wherein the amino acid sequence of the isolated polypeptideis SEQ ID NO:
 183. 81. The isolated polypeptide of claim 8, wherein theamino acid sequence of the isolated polypeptide is SEQ ID NO:
 243. 82.The isolated polypeptide of claim 8, wherein the amino acid sequence ofthe isolated polypeptide is SEQ ID NO:
 253. 83. The isolated polypeptideof claim 8, wherein the amino acid sequence of the isolated polypeptideis SEQ ID NO:
 363. 84. The isolated polypeptide of claim 8, wherein theamino acid sequence of the isolated polypeptide is SEQ ID NO:
 353. 85.The isolated polypeptide of claim 8, wherein the amino acid sequence ofthe isolated polypeptide is SEQ ID NO: 439.